diff --git a/jcvi/algorithms/supermap.py b/jcvi/algorithms/supermap.py
index f728341c..cef9e994 100755
--- a/jcvi/algorithms/supermap.py
+++ b/jcvi/algorithms/supermap.py
@@ -147,14 +147,14 @@ def supermap(blast_file, filter="intersection", dialect="blast", clip=0):
 
     filter_choices = ("ref", "query", "intersection", "union")
     dialect_choices = ("blast", "coords")
-    p.add_option(
+    p.add_argument(
         "--filter",
         choices=filter_choices,
         default="intersection",
         help="Available filters",
     )
-    p.add_option("--dialect", choices=dialect_choices, help="Input format")
-    p.add_option(
+    p.add_argument("--dialect", choices=dialect_choices, help="Input format")
+    p.add_argument(
         "--clip",
         default=0,
         type=int,
diff --git a/jcvi/annotation/ahrd.py b/jcvi/annotation/ahrd.py
index ae39c3f7..cfdb1598 100644
--- a/jcvi/annotation/ahrd.py
+++ b/jcvi/annotation/ahrd.py
@@ -554,7 +554,7 @@ def fix(args):
     Fix ugly names from Uniprot.
     """
     p = OptionParser(fix.__doc__)
-    p.add_option(
+    p.add_argument(
         "--ignore_sym_pat",
         default=False,
         action="store_true",
@@ -650,19 +650,19 @@ def batch(args):
     ahrd_weights = {"blastp": [0.5, 0.3, 0.2], "blastx": [0.6, 0.4, 0.0]}
     blast_progs = tuple(ahrd_weights.keys())
 
-    p.add_option(
+    p.add_argument(
         "--path",
         default="~/code/AHRD/",
         help="Path where AHRD is installed",
     )
-    p.add_option(
+    p.add_argument(
         "--blastprog",
         default="blastp",
         choices=blast_progs,
         help="Specify the blast program being run. Based on this option,"
         + " the AHRD parameters (score_weights) will be modified",
     )
-    p.add_option(
+    p.add_argument(
         "--iprscan",
         default=None,
         help="Specify path to InterProScan results file if available."
diff --git a/jcvi/annotation/automaton.py b/jcvi/annotation/automaton.py
index ef2ec0a7..7db98a42 100644
--- a/jcvi/annotation/automaton.py
+++ b/jcvi/annotation/automaton.py
@@ -63,9 +63,13 @@ def augustus(args):
     annotation.reformat.augustus().
     """
     p = OptionParser(augustus.__doc__)
-    p.add_option("--species", default="maize", help="Use species model for prediction")
-    p.add_option("--hintsfile", help="Hint-guided AUGUSTUS")
-    p.add_option("--nogff3", default=False, action="store_true", help="Turn --gff3=off")
+    p.add_argument(
+        "--species", default="maize", help="Use species model for prediction"
+    )
+    p.add_argument("--hintsfile", help="Hint-guided AUGUSTUS")
+    p.add_argument(
+        "--nogff3", default=False, action="store_true", help="Turn --gff3=off"
+    )
     p.set_home("augustus")
     p.set_cpus()
     opts, args = p.parse_args(args)
@@ -112,7 +116,7 @@ def star(args):
     Run star on a folder with reads.
     """
     p = OptionParser(star.__doc__)
-    p.add_option(
+    p.add_argument(
         "--single", default=False, action="store_true", help="Single end mapping"
     )
     p.set_fastq_names()
@@ -163,7 +167,7 @@ def cufflinks(args):
     Run cufflinks on a folder containing tophat results.
     """
     p = OptionParser(cufflinks.__doc__)
-    p.add_option("--gtf", help="Reference annotation")
+    p.add_argument("--gtf", help="Reference annotation")
     p.set_cpus()
     opts, args = p.parse_args(args)
 
@@ -219,23 +223,23 @@ def tophat(args):
     from jcvi.formats.fastq import guessoffset
 
     p = OptionParser(tophat.__doc__)
-    p.add_option("--gtf", help="Reference annotation")
-    p.add_option(
+    p.add_argument("--gtf", help="Reference annotation")
+    p.add_argument(
         "--single", default=False, action="store_true", help="Single end mapping"
     )
-    p.add_option(
+    p.add_argument(
         "--intron",
         default=15000,
         type=int,
         help="Max intron size",
     )
-    p.add_option(
+    p.add_argument(
         "--dist",
         default=-50,
         type=int,
         help="Mate inner distance",
     )
-    p.add_option(
+    p.add_argument(
         "--stdev",
         default=50,
         type=int,
diff --git a/jcvi/annotation/depth.py b/jcvi/annotation/depth.py
index 84acfe4f..6aaf151a 100755
--- a/jcvi/annotation/depth.py
+++ b/jcvi/annotation/depth.py
@@ -64,13 +64,13 @@ def bed(args):
     Write bed files where the bases have at least certain depth.
     """
     p = OptionParser(bed.__doc__)
-    p.add_option(
+    p.add_argument(
         "-o",
         dest="output",
         default="stdout",
         help="Output file name",
     )
-    p.add_option(
+    p.add_argument(
         "--cutoff",
         dest="cutoff",
         default=10,
diff --git a/jcvi/annotation/maker.py b/jcvi/annotation/maker.py
index 09284f39..0f3fab4c 100644
--- a/jcvi/annotation/maker.py
+++ b/jcvi/annotation/maker.py
@@ -351,7 +351,7 @@ def batcheval(args):
     from jcvi.formats.gff import make_index
 
     p = OptionParser(evaluate.__doc__)
-    p.add_option(
+    p.add_argument(
         "--type",
         default="CDS",
         help="list of features to extract, use comma to separate (e.g."
@@ -450,17 +450,17 @@ def split(args):
     from jcvi.formats.bed import Bed
 
     p = OptionParser(split.__doc__)
-    p.add_option(
+    p.add_argument(
         "--key",
         default="Name",
         help="Key in the attributes to extract predictor.gff",
     )
-    p.add_option(
+    p.add_argument(
         "--parents",
         default="match",
         help="list of features to extract, use comma to separate (e.g.'gene,mRNA')",
     )
-    p.add_option(
+    p.add_argument(
         "--children",
         default="match_part",
         help="list of features to extract, use comma to separate (e.g."
diff --git a/jcvi/annotation/pasa.py b/jcvi/annotation/pasa.py
index a5c6ce5d..c23f0eb0 100644
--- a/jcvi/annotation/pasa.py
+++ b/jcvi/annotation/pasa.py
@@ -81,7 +81,7 @@ def assemble(args):
     """
     p = OptionParser(assemble.__doc__)
     p.set_pasa_opts()
-    p.add_option(
+    p.add_argument(
         "--prepare",
         default=False,
         action="store_true",
@@ -228,7 +228,7 @@ def compare(args):
     """
     p = OptionParser(compare.__doc__)
     p.set_pasa_opts(action="compare")
-    p.add_option(
+    p.add_argument(
         "--prepare",
         default=False,
         action="store_true",
@@ -320,7 +320,7 @@ def longest(args):
     from jcvi.formats.sizes import Sizes
 
     p = OptionParser(longest.__doc__)
-    p.add_option(
+    p.add_argument(
         "--prefix",
         default="pasa",
         help="Replace asmbl_ with prefix",
@@ -393,31 +393,31 @@ def consolidate(args):
 
     supported_modes = ["name", "coords"]
     p = OptionParser(consolidate.__doc__)
-    p.add_option(
+    p.add_argument(
         "--slop",
         default=False,
         action="store_true",
         help="allow minor variation in terminal 5'/3' UTR start/stop position",
     )
-    p.add_option(
+    p.add_argument(
         "--inferUTR",
         default=False,
         action="store_true",
         help="infer presence of UTRs from exon coordinates",
     )
-    p.add_option(
+    p.add_argument(
         "--mode",
         default="name",
         choices=supported_modes,
         help="method used to determine overlapping loci",
     )
-    p.add_option(
+    p.add_argument(
         "--summary",
         default=False,
         action="store_true",
         help="Generate summary table of consolidation process",
     )
-    p.add_option(
+    p.add_argument(
         "--clusters",
         default=False,
         action="store_true",
diff --git a/jcvi/annotation/qc.py b/jcvi/annotation/qc.py
index fcb3e74b..825730dd 100644
--- a/jcvi/annotation/qc.py
+++ b/jcvi/annotation/qc.py
@@ -165,26 +165,26 @@ def trimUTR(args):
     from jcvi.formats.base import SetFile
 
     p = OptionParser(trimUTR.__doc__)
-    p.add_option(
+    p.add_argument(
         "--trim5",
         default=None,
         type=str,
         help="File containing gene list for 5' UTR trimming",
     )
-    p.add_option(
+    p.add_argument(
         "--trim3",
         default=None,
         type=str,
         help="File containing gene list for 3' UTR trimming",
     )
-    p.add_option(
+    p.add_argument(
         "--trimrange",
         default=None,
         type=str,
         help="File containing gene list for UTR trim back"
         + "based on suggested (start, stop) coordinate range",
     )
-    p.add_option(
+    p.add_argument(
         "--refgff",
         default=None,
         type=str,
diff --git a/jcvi/annotation/reformat.py b/jcvi/annotation/reformat.py
index 40409597..cb68db5c 100644
--- a/jcvi/annotation/reformat.py
+++ b/jcvi/annotation/reformat.py
@@ -209,9 +209,9 @@ def plot(args):
     from jcvi.graphics.chromosome import ChromosomeMap
 
     p = OptionParser(plot.__doc__)
-    p.add_option("--firstn", type=int, help="Only plot the first N genes")
-    p.add_option("--ymax", type=int, help="Y-axis max value")
-    p.add_option("--log", action="store_true", help="Write plotting data")
+    p.add_argument("--firstn", type=int, help="Only plot the first N genes")
+    p.add_argument("--ymax", type=int, help="Y-axis max value")
+    p.add_argument("--log", action="store_true", help="Write plotting data")
     opts, args, iopts = p.set_image_options(args, figsize="6x4")
 
     if len(args) != 2:
@@ -305,7 +305,7 @@ def instantiate(args):
     """
     p = OptionParser(instantiate.__doc__)
     p.set_annot_reformat_opts()
-    p.add_option(
+    p.add_argument(
         "--extended_stride",
         default=False,
         action="store_true",
@@ -594,13 +594,13 @@ def annotate(args):
     valid_resolve_choices = ["alignment", "overlap"]
 
     p = OptionParser(annotate.__doc__)
-    p.add_option(
+    p.add_argument(
         "--resolve",
         default="alignment",
         choices=valid_resolve_choices,
         help="Resolve ID assignment based on a certain metric",
     )
-    p.add_option(
+    p.add_argument(
         "--atg_name",
         default=False,
         action="store_true",
@@ -611,14 +611,14 @@ def annotate(args):
         "Optional parameters (alignment):\n"
         + "Use if resolving ambiguities based on sequence `alignment`",
     )
-    g1.add_option(
+    g1.add_argument(
         "--pid",
         dest="pid",
         default=35.0,
         type=float,
         help="Percent identity cutoff",
     )
-    g1.add_option(
+    g1.add_argument(
         "--score",
         dest="score",
         default=250.0,
@@ -631,21 +631,21 @@ def annotate(args):
         + "Use if resolving ambiguities based on `overlap` length\n"
         + "Parameters equivalent to `intersectBed`",
     )
-    g2.add_option(
+    g2.add_argument(
         "-f",
         dest="f",
         default=0.5,
         type=float,
         help="Minimum overlap fraction (0.0 - 1.0)",
     )
-    g2.add_option(
+    g2.add_argument(
         "-r",
         dest="r",
         default=False,
         action="store_true",
         help="Require fraction overlap to be reciprocal",
     )
-    g2.add_option(
+    g2.add_argument(
         "-s",
         dest="s",
         default=True,
@@ -944,34 +944,34 @@ def rename(args):
     import string
 
     p = OptionParser(rename.__doc__)
-    p.add_option(
+    p.add_argument(
         "-a",
         dest="gene_increment",
         default=10,
         type=int,
         help="Increment for continuous genes",
     )
-    p.add_option(
+    p.add_argument(
         "-b",
         dest="gap_increment",
         default=1000,
         type=int,
         help="Increment for gaps",
     )
-    p.add_option(
+    p.add_argument(
         "--pad0",
         default=6,
         type=int,
         help="Pad gene identifiers with 0",
     )
-    p.add_option(
+    p.add_argument(
         "--spad0",
         default=4,
         type=int,
         help="Pad gene identifiers on small scaffolds",
     )
-    p.add_option("--prefix", default="Bo", help="Genome prefix")
-    p.add_option(
+    p.add_argument("--prefix", default="Bo", help="Genome prefix")
+    p.add_argument(
         "--jgi",
         default=False,
         action="store_true",
@@ -1072,7 +1072,7 @@ def reindex(args):
     from tempfile import mkstemp
 
     p = OptionParser(reindex.__doc__)
-    p.add_option(
+    p.add_argument(
         "--scores", type=str, help="read from existing EMBOSS `needle` scores file"
     )
     p.set_outfile()
@@ -1235,7 +1235,7 @@ def publocus(args):
     Medtr1g007060.2		MTR_1g007060B
     """
     p = OptionParser(publocus.__doc__)
-    p.add_option("--locus_tag", default="MTR_", help="GenBank locus tag")
+    p.add_argument("--locus_tag", default="MTR_", help="GenBank locus tag")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
diff --git a/jcvi/annotation/stats.py b/jcvi/annotation/stats.py
index 6f8025d7..ec477ab5 100644
--- a/jcvi/annotation/stats.py
+++ b/jcvi/annotation/stats.py
@@ -147,7 +147,9 @@ def genestats(args):
     A physical, genetic and functional sequence assembly of the barley genome
     """
     p = OptionParser(genestats.__doc__)
-    p.add_option("--groupby", default="conf_class", help="Print separate stats groupby")
+    p.add_argument(
+        "--groupby", default="conf_class", help="Print separate stats groupby"
+    )
     p.set_outfile()
     opts, args = p.parse_args(args)
 
@@ -286,7 +288,7 @@ def histogram(args):
     from jcvi.graphics.histogram import histogram_multiple
 
     p = OptionParser(histogram.__doc__)
-    p.add_option(
+    p.add_argument(
         "--bins",
         dest="bins",
         default=40,
@@ -338,8 +340,8 @@ def stats(args):
     With data written to disk then you can run %prog histogram
     """
     p = OptionParser(stats.__doc__)
-    p.add_option("--gene", default="mRNA", help="The gene type")
-    p.add_option("--exon", default="CDS", help="The exon type")
+    p.add_argument("--gene", default="mRNA", help="The gene type")
+    p.add_argument("--exon", default="CDS", help="The exon type")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
diff --git a/jcvi/annotation/train.py b/jcvi/annotation/train.py
index 45e30b2f..9ef54431 100644
--- a/jcvi/annotation/train.py
+++ b/jcvi/annotation/train.py
@@ -89,7 +89,7 @@ def genemark(args):
     model gff file is needed.
     """
     p = OptionParser(genemark.__doc__)
-    p.add_option("--junctions", help="Path to `junctions.bed` from Tophat2")
+    p.add_argument("--junctions", help="Path to `junctions.bed` from Tophat2")
     p.set_home("gmes")
     p.set_cpus(cpus=32)
     opts, args = p.parse_args(args)
@@ -168,7 +168,7 @@ def augustus(args):
     <http://www.molecularevolution.org/molevolfiles/exercises/augustus/training.html>
     """
     p = OptionParser(augustus.__doc__)
-    p.add_option(
+    p.add_argument(
         "--autotrain",
         default=False,
         action="store_true",
diff --git a/jcvi/annotation/trinity.py b/jcvi/annotation/trinity.py
index 812683b9..1f742501 100644
--- a/jcvi/annotation/trinity.py
+++ b/jcvi/annotation/trinity.py
@@ -43,13 +43,13 @@ def prepare(args):
     If "--merge" is specified, the fastq files are merged together before assembling
     """
     p = OptionParser(prepare.__doc__)
-    p.add_option(
+    p.add_argument(
         "--paired",
         default=False,
         action="store_true",
         help="Paired-end mode",
     )
-    p.add_option(
+    p.add_argument(
         "--merge",
         default=False,
         action="store_true",
diff --git a/jcvi/apps/align.py b/jcvi/apps/align.py
index 6e96831b..54e3f7a8 100644
--- a/jcvi/apps/align.py
+++ b/jcvi/apps/align.py
@@ -157,7 +157,7 @@ def minimap(args):
     from jcvi.formats.fasta import Fasta
 
     p = OptionParser(minimap.__doc__)
-    p.add_option(
+    p.add_argument(
         "--chunks",
         type=int,
         default=2000000,
@@ -216,7 +216,9 @@ def nucmer(args):
     from jcvi.formats.base import split
 
     p = OptionParser(nucmer.__doc__)
-    p.add_option("--chunks", type=int, help="Split both query and subject into chunks")
+    p.add_argument(
+        "--chunks", type=int, help="Split both query and subject into chunks"
+    )
     p.set_params(prog="nucmer", params="-l 100 -c 500")
     p.set_cpus()
     opts, args = p.parse_args(args)
@@ -350,9 +352,9 @@ def blast(args):
     task_choices = ("blastn", "blastn-short", "dc-megablast", "megablast", "vecscreen")
     p = OptionParser(blast.__doc__)
     p.set_align(pctid=0, evalue=0.01)
-    p.add_option("--wordsize", type=int, help="Word size")
-    p.add_option("--best", default=1, type=int, help="Only look for best N hits")
-    p.add_option(
+    p.add_argument("--wordsize", type=int, help="Word size")
+    p.add_argument("--best", default=1, type=int, help="Only look for best N hits")
+    p.add_argument(
         "--task", default="megablast", choices=task_choices, help="Task of the blastn"
     )
     p.set_cpus()
@@ -489,29 +491,29 @@ def last(args, dbtype=None):
     Works with LAST-719.
     """
     p = OptionParser(last.__doc__)
-    p.add_option(
+    p.add_argument(
         "--dbtype",
         default="nucl",
         choices=("nucl", "prot"),
         help="Molecule type of subject database",
     )
-    p.add_option("--path", help="Specify LAST path")
-    p.add_option(
+    p.add_argument("--path", help="Specify LAST path")
+    p.add_argument(
         "--mask", default=False, action="store_true", help="Invoke -c in lastdb"
     )
-    p.add_option(
+    p.add_argument(
         "--format",
         default="BlastTab",
         choices=("TAB", "MAF", "BlastTab", "BlastTab+"),
         help="Output format",
     )
-    p.add_option(
+    p.add_argument(
         "--minlen",
         default=0,
         type=int,
         help="Filter alignments by how many bases match",
     )
-    p.add_option("--minid", default=0, type=int, help="Minimum sequence identity")
+    p.add_argument("--minid", default=0, type=int, help="Minimum sequence identity")
     p.set_cpus()
     p.set_outdir()
     p.set_params()
@@ -598,13 +600,13 @@ def blast_main(args, dbtype=None):
     Run blastp/blastn by calling BLAST+ blastp/blastn depends on dbtype.
     """
     p = OptionParser(blast_main.__doc__)
-    p.add_option(
+    p.add_argument(
         "--dbtype",
         default="nucl",
         choices=("nucl", "prot"),
         help="Molecule type of subject database",
     )
-    p.add_option("--path", help="Specify BLAST path for blastn or blastp")
+    p.add_argument("--path", help="Specify BLAST path for blastn or blastp")
 
     p.set_cpus()
     p.set_outdir()
@@ -662,7 +664,7 @@ def diamond_blastp_main(args, dbtype="prot"):
     """
     p = OptionParser(diamond_blastp_main.__doc__)
 
-    p.add_option("--path", help="Specify diamond path for diamond blastp")
+    p.add_argument("--path", help="Specify diamond path for diamond blastp")
 
     p.set_cpus()
     p.set_outdir()
diff --git a/jcvi/apps/base.py b/jcvi/apps/base.py
index bbaa17ad..3fa3cc32 100644
--- a/jcvi/apps/base.py
+++ b/jcvi/apps/base.py
@@ -154,14 +154,6 @@ class OptionParser(ArgumentParser):
     def __init__(self, doc: Optional[str]):
         super(OptionParser, self).__init__(doc, epilog=JCVIHELP)
 
-    def add_option(self, *args, **kwargs):
-        """
-        Add an option to the parser.
-        """
-        if "help" in kwargs:
-            kwargs["help"] = kwargs["help"].replace("%prog", self.prog)
-        return self.add_argument(*args, **kwargs)
-
     def parse_args(self, args=None):
         """
         Parse the command line arguments.
diff --git a/jcvi/apps/biomart.py b/jcvi/apps/biomart.py
index f934aadb..e10ade33 100644
--- a/jcvi/apps/biomart.py
+++ b/jcvi/apps/biomart.py
@@ -123,7 +123,7 @@ def parse_configuration(self):
         for t in self.getiterator("FilterDescription"):
             f = Filter(**t.attrib)
             options = [Option(**x.attrib) for x in t.getiterator("Option")]
-            f.add_options(options)
+            f.add_arguments(options)
             yield f
 
 
@@ -317,7 +317,7 @@ class Filter(MartArgument):
     then use the filter chromosome_name with value `1`
     """
 
-    def add_options(self, options):
+    def add_arguments(self, options):
         self.options = dict((x.displayName, x) for x in options)
 
 
diff --git a/jcvi/apps/blastplus.py b/jcvi/apps/blastplus.py
index 5a7295c9..5756596e 100755
--- a/jcvi/apps/blastplus.py
+++ b/jcvi/apps/blastplus.py
@@ -36,19 +36,19 @@ def main():
     """
     p = OptionParser(main.__doc__)
 
-    p.add_option(
+    p.add_argument(
         "--format",
         default=" '6 qseqid sseqid pident length "
         "mismatch gapopen qstart qend sstart send evalue bitscore' ",
         help='0-11, learn more with "blastp -help"',
     )
-    p.add_option(
+    p.add_argument(
         "--path",
         dest="blast_path",
         default=None,
         help="specify BLAST+ path including the program name",
     )
-    p.add_option(
+    p.add_argument(
         "--prog",
         dest="blast_program",
         default="blastp",
@@ -56,14 +56,14 @@ def main():
         "http://www.ncbi.nlm.nih.gov/books/NBK52640/#chapter1.Installation",
     )
     p.set_align(evalue=0.01)
-    p.add_option(
+    p.add_argument(
         "--best",
         default=1,
         type=int,
         help="Only look for best N hits",
     )
     p.set_cpus()
-    p.add_option(
+    p.add_argument(
         "--nprocs",
         default=1,
         type=int,
diff --git a/jcvi/apps/bowtie.py b/jcvi/apps/bowtie.py
index a7f1f3aa..06a3a3c8 100644
--- a/jcvi/apps/bowtie.py
+++ b/jcvi/apps/bowtie.py
@@ -98,25 +98,25 @@ def align(args):
 
     p = OptionParser(align.__doc__)
     p.set_firstN(firstN=0)
-    p.add_option(
+    p.add_argument(
         "--full",
         default=False,
         action="store_true",
         help="Enforce end-to-end alignment [default: local]",
     )
-    p.add_option(
+    p.add_argument(
         "--reorder",
         default=False,
         action="store_true",
         help="Keep the input read order",
     )
-    p.add_option(
+    p.add_argument(
         "--null",
         default=False,
         action="store_true",
         help="Do not write to SAM/BAM output",
     )
-    p.add_option(
+    p.add_argument(
         "--fasta", default=False, action="store_true", help="Query reads are FASTA"
     )
     p.set_cutoff(cutoff=800)
diff --git a/jcvi/apps/bwa.py b/jcvi/apps/bwa.py
index 974a2696..45ccfd13 100644
--- a/jcvi/apps/bwa.py
+++ b/jcvi/apps/bwa.py
@@ -124,9 +124,9 @@ def index(args):
 
 def set_align_options(p):
     """Used in align() and batch()"""
-    p.add_option("--bwa", default="bwa", help="Run bwa at this path")
-    p.add_option("--rg", help="Read group")
-    p.add_option(
+    p.add_argument("--bwa", default="bwa", help="Run bwa at this path")
+    p.add_argument("--rg", help="Read group")
+    p.add_argument(
         "--readtype",
         choices=("pacbio", "pbread", "ont2d", "intractg"),
         help="Read type in bwa-mem",
@@ -142,7 +142,7 @@ def align(args):
     """
     valid_modes = ("bwasw", "aln", "mem")
     p = OptionParser(align.__doc__)
-    p.add_option("--mode", default="mem", choices=valid_modes, help="BWA mode")
+    p.add_argument("--mode", default="mem", choices=valid_modes, help="BWA mode")
     set_align_options(p)
     p.set_sam_options()
 
diff --git a/jcvi/apps/cdhit.py b/jcvi/apps/cdhit.py
index 686576e2..65f1bd3c 100644
--- a/jcvi/apps/cdhit.py
+++ b/jcvi/apps/cdhit.py
@@ -84,7 +84,7 @@ def filter(args):
     from jcvi.formats.fasta import Fasta, SeqIO
 
     p = OptionParser(filter.__doc__)
-    p.add_option("--minsize", default=2, type=int, help="Minimum cluster size")
+    p.add_argument("--minsize", default=2, type=int, help="Minimum cluster size")
     p.set_outfile()
     opts, args = p.parse_args(args)
 
@@ -136,7 +136,7 @@ def ids(args):
     Get the representative ids from clstr file.
     """
     p = OptionParser(ids.__doc__)
-    p.add_option("--prefix", type=int, help="Find rep id for prefix of len")
+    p.add_argument("--prefix", type=int, help="Find rep id for prefix of len")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -192,25 +192,25 @@ def deduplicate(args):
     """
     p = OptionParser(deduplicate.__doc__)
     p.set_align(pctid=96, pctcov=0)
-    p.add_option(
+    p.add_argument(
         "--fast",
         default=False,
         action="store_true",
         help="Place sequence in the first cluster",
     )
-    p.add_option(
+    p.add_argument(
         "--consensus",
         default=False,
         action="store_true",
         help="Compute consensus sequences",
     )
-    p.add_option(
+    p.add_argument(
         "--reads",
         default=False,
         action="store_true",
         help="Use `cd-hit-454` to deduplicate",
     )
-    p.add_option(
+    p.add_argument(
         "--samestrand",
         default=False,
         action="store_true",
diff --git a/jcvi/apps/fetch.py b/jcvi/apps/fetch.py
index 876646c2..9ae25a3b 100644
--- a/jcvi/apps/fetch.py
+++ b/jcvi/apps/fetch.py
@@ -148,7 +148,7 @@ def ensembl(args):
     $ %prog ensembl danio_rerio,gasterosteus_aculeatus
     """
     p = OptionParser(ensembl.__doc__)
-    p.add_option("--version", default="75", help="Ensembl version")
+    p.add_argument("--version", default="75", help="Ensembl version")
     opts, args = p.parse_args(args)
 
     version = opts.version
@@ -227,19 +227,19 @@ def phytozome(args):
     from jcvi.apps.biomart import GlobusXMLParser
 
     p = OptionParser(phytozome.__doc__)
-    p.add_option(
+    p.add_argument(
         "--version",
         default="12",
         choices=("9", "10", "11", "12", "12_unrestricted", "13"),
         help="Phytozome version",
     )
-    p.add_option(
+    p.add_argument(
         "--assembly",
         default=False,
         action="store_true",
         help="Download assembly",
     )
-    p.add_option(
+    p.add_argument(
         "--format",
         default=False,
         action="store_true",
@@ -363,13 +363,13 @@ def phytozome9(args):
     $ %prog phytozome9 Athaliana,Vvinifera,Osativa,Sbicolor,Slycopersicum
     """
     p = OptionParser(phytozome9.__doc__)
-    p.add_option(
+    p.add_argument(
         "--assembly",
         default=False,
         action="store_true",
         help="Download assembly",
     )
-    p.add_option(
+    p.add_argument(
         "--format",
         default=False,
         action="store_true",
@@ -545,45 +545,45 @@ def entrez(args):
     valid_formats = tuple(allowed_databases.keys())
     valid_databases = ("genome", "nuccore", "nucest", "nucgss", "protein", "gene")
 
-    p.add_option(
+    p.add_argument(
         "--noversion",
         dest="noversion",
         default=False,
         action="store_true",
         help="Remove trailing accession versions",
     )
-    p.add_option(
+    p.add_argument(
         "--format",
         default="fasta",
         choices=valid_formats,
         help="download format",
     )
-    p.add_option(
+    p.add_argument(
         "--database",
         default="nuccore",
         choices=valid_databases,
         help="search database",
     )
-    p.add_option(
+    p.add_argument(
         "--retmax",
         default=1000000,
         type=int,
         help="how many results to return",
     )
-    p.add_option(
+    p.add_argument(
         "--skipcheck",
         default=False,
         action="store_true",
         help="turn off prompt to check file existence",
     )
-    p.add_option(
+    p.add_argument(
         "--batchsize",
         default=500,
         type=int,
         help="download the results in batch for speed-up",
     )
     p.set_outdir(outdir=None)
-    p.add_option("--outprefix", default="out", help="output file name prefix")
+    p.add_argument("--outprefix", default="out", help="output file name prefix")
     p.set_email()
     opts, args = p.parse_args(args)
 
@@ -674,7 +674,7 @@ def sra(args):
     """
     p = OptionParser(sra.__doc__)
 
-    p.add_option(
+    p.add_argument(
         "--nogzip",
         dest="nogzip",
         default=False,
diff --git a/jcvi/apps/gbsubmit.py b/jcvi/apps/gbsubmit.py
index c98524d5..bbfb5260 100644
--- a/jcvi/apps/gbsubmit.py
+++ b/jcvi/apps/gbsubmit.py
@@ -135,7 +135,7 @@ def fcs(args):
     contig0800      124133  30512..30559    primer/adapter
     """
     p = OptionParser(fcs.__doc__)
-    p.add_option(
+    p.add_argument(
         "--cutoff",
         default=200,
         help="Skip small components less than",
@@ -259,7 +259,7 @@ def htgnew(args):
     from jcvi.formats.fasta import sequin
 
     p = OptionParser(htgnew.__doc__)
-    p.add_option("--comment", default="", help="Comments for this submission")
+    p.add_argument("--comment", default="", help="Comments for this submission")
     opts, args = p.parse_args(args)
 
     if len(args) != 3:
@@ -358,12 +358,12 @@ def htg(args):
     from jcvi.apps.fetch import entrez
 
     p = OptionParser(htg.__doc__)
-    p.add_option(
+    p.add_argument(
         "--phases",
         default=None,
         help="Use another phasefile to override",
     )
-    p.add_option("--comment", default="", help="Comments for this update")
+    p.add_argument("--comment", default="", help="Comments for this update")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
diff --git a/jcvi/apps/gmap.py b/jcvi/apps/gmap.py
index 2bd51875..f952e220 100644
--- a/jcvi/apps/gmap.py
+++ b/jcvi/apps/gmap.py
@@ -113,7 +113,7 @@ def index(args):
         Wrapper for `gmap_build`. Same interface.
     """
     p = OptionParser(index.__doc__)
-    p.add_option(
+    p.add_argument(
         "--supercat",
         default=False,
         action="store_true",
@@ -135,10 +135,10 @@ def gmap(args):
     Wrapper for `gmap`.
     """
     p = OptionParser(gmap.__doc__)
-    p.add_option(
+    p.add_argument(
         "--cross", default=False, action="store_true", help="Cross-species alignment"
     )
-    p.add_option(
+    p.add_argument(
         "--npaths",
         default=0,
         type=int,
@@ -185,13 +185,13 @@ def align(args):
     from jcvi.formats.fastq import guessoffset
 
     p = OptionParser(align.__doc__)
-    p.add_option(
+    p.add_argument(
         "--rnaseq",
         default=False,
         action="store_true",
         help="Input is RNA-seq reads, turn splicing on",
     )
-    p.add_option(
+    p.add_argument(
         "--native",
         default=False,
         action="store_true",
diff --git a/jcvi/apps/grid.py b/jcvi/apps/grid.py
index e7c8ffd2..06230a04 100644
--- a/jcvi/apps/grid.py
+++ b/jcvi/apps/grid.py
@@ -618,7 +618,7 @@ def kill(args):
 
     valid_methods = ("pattern", "jobid")
     p = OptionParser(kill.__doc__)
-    p.add_option(
+    p.add_argument(
         "--method",
         choices=valid_methods,
         help="Identify jobs based on [default: guess]",
diff --git a/jcvi/apps/lastz.py b/jcvi/apps/lastz.py
index acdc1a71..0b725f92 100755
--- a/jcvi/apps/lastz.py
+++ b/jcvi/apps/lastz.py
@@ -183,21 +183,21 @@ def main():
         "sam-, softsam-, cigar, BLASTN, BLASTN-, differences, rdotplot, text".split(",")
     )
 
-    p.add_option(
+    p.add_argument(
         "--format",
         default="BLASTN-",
         choices=supported_formats,
         help="Ooutput format",
     )
-    p.add_option("--path", dest="lastz_path", default=None, help="specify LASTZ path")
-    p.add_option(
+    p.add_argument("--path", dest="lastz_path", default=None, help="specify LASTZ path")
+    p.add_argument(
         "--mask",
         dest="mask",
         default=False,
         action="store_true",
         help="treat lower-case letters as mask info",
     )
-    p.add_option(
+    p.add_argument(
         "--similar",
         default=False,
         action="store_true",
diff --git a/jcvi/apps/mask.py b/jcvi/apps/mask.py
index 3fdb8bfb..126ea817 100755
--- a/jcvi/apps/mask.py
+++ b/jcvi/apps/mask.py
@@ -96,7 +96,7 @@ def mask(args):
     (default to lower case, set --hard for hardmasking).
     """
     p = OptionParser(mask.__doc__)
-    p.add_option(
+    p.add_argument(
         "--hard",
         dest="hard",
         default=False,
diff --git a/jcvi/apps/phylo.py b/jcvi/apps/phylo.py
index 90b0e76e..f0127fad 100644
--- a/jcvi/apps/phylo.py
+++ b/jcvi/apps/phylo.py
@@ -701,8 +701,8 @@ def prepare(args):
     from jcvi.graphics.base import discrete_rainbow
 
     p = OptionParser(prepare.__doc__)
-    p.add_option("--addtandem", help="path to tandemfile")
-    p.add_option(
+    p.add_argument("--addtandem", help="path to tandemfile")
+    p.add_argument(
         "--writecolors",
         default=False,
         action="store_true",
@@ -819,53 +819,53 @@ def build(args):
     from jcvi.formats.fasta import translate
 
     p = OptionParser(build.__doc__)
-    p.add_option(
+    p.add_argument(
         "--longest",
         action="store_true",
         help="Get longest ORF, only works if no pep file, e.g. ESTs",
     )
-    p.add_option(
+    p.add_argument(
         "--nogblocks",
         action="store_true",
         help="don't use Gblocks to edit alignment",
     )
-    p.add_option(
+    p.add_argument(
         "--synonymous",
         action="store_true",
         help="extract synonymous sites of the alignment",
     )
-    p.add_option(
+    p.add_argument(
         "--fourfold",
         action="store_true",
         help="extract fourfold degenerate sites of the alignment",
     )
-    p.add_option(
+    p.add_argument(
         "--msa",
         default="muscle",
         choices=("clustalw", "muscle"),
         help="software used to align the proteins",
     )
-    p.add_option(
+    p.add_argument(
         "--noneighbor",
         action="store_true",
         help="don't build NJ tree",
     )
-    p.add_option(
+    p.add_argument(
         "--ml",
         default=None,
         choices=("raxml", "phyml"),
         help="software used to build ML tree",
     )
-    p.add_option("--outgroup", help="path to file containing outgroup orders")
-    p.add_option("--SH", help="path to reference Newick tree")
-    p.add_option("--shout", default="SH_out.txt", help="SH output file name")
-    p.add_option(
+    p.add_argument("--outgroup", help="path to file containing outgroup orders")
+    p.add_argument("--SH", help="path to reference Newick tree")
+    p.add_argument("--shout", default="SH_out.txt", help="SH output file name")
+    p.add_argument(
         "--treefix",
         action="store_true",
         help="use TreeFix to rearrange ML tree",
     )
-    p.add_option("--stree", help="path to species Newick tree")
-    p.add_option(
+    p.add_argument("--stree", help="path to species Newick tree")
+    p.add_argument(
         "--smap",
         help="path to smap file: gene_name_pattern<tab>species_name",
     )
@@ -1085,18 +1085,18 @@ def draw(args):
     """
     trunc_name_options = ["headn", "oheadn", "tailn", "otailn"]
     p = OptionParser(draw.__doc__)
-    p.add_option(
+    p.add_argument(
         "--input",
         help="path to single input tree file or a dir "
         "containing ONLY the input tree files",
     )
-    p.add_option(
+    p.add_argument(
         "--combine",
         type=str,
         default="1x1",
         help="combine multiple trees into one plot in nrowxncol",
     )
-    p.add_option(
+    p.add_argument(
         "--trunc_name",
         default=None,
         help="Options are: {0}. "
@@ -1104,27 +1104,27 @@ def draw(args):
         "truncate last n chars, retain only last chars. "
         "n=1~99.".format(trunc_name_options),
     )
-    p.add_option(
+    p.add_argument(
         "--SH",
         default=None,
         help="path to a file containing SH test p-values in format:"
         "tree_file_name<tab>p-values "
         "This file can be generated with jcvi.apps.phylo build",
     )
-    p.add_option(
+    p.add_argument(
         "--scutoff",
         default=50,
         type=int,
         help="cutoff for displaying node support, 0-100",
     )
-    p.add_option(
+    p.add_argument(
         "--barcode",
         default=None,
         help="path to seq/taxon name barcode mapping file: "
         "barcode<tab>new_name "
         "This option is downstream of `--trunc_name`",
     )
-    p.add_option(
+    p.add_argument(
         "--leafcolorfile",
         default=None,
         help="path to a mapping file containing font colors "
diff --git a/jcvi/apps/restriction.py b/jcvi/apps/restriction.py
index a8544c12..42e901d0 100644
--- a/jcvi/apps/restriction.py
+++ b/jcvi/apps/restriction.py
@@ -125,13 +125,13 @@ def fragment(args):
     ends are NOT extracted, as in the first fragment.
     """
     p = OptionParser(fragment.__doc__)
-    p.add_option(
+    p.add_argument(
         "--flank",
         default=150,
         type=int,
         help="Extract flanking bases of the cut sites",
     )
-    p.add_option(
+    p.add_argument(
         "--full",
         default=False,
         action="store_true",
diff --git a/jcvi/apps/softlink.py b/jcvi/apps/softlink.py
index 934f5e21..9ef12b7a 100644
--- a/jcvi/apps/softlink.py
+++ b/jcvi/apps/softlink.py
@@ -43,7 +43,7 @@ def link(args):
     from jcvi.apps.base import mkdir
 
     p = OptionParser(link.__doc__)
-    p.add_option("--dir", help="Place links in a subdirectory")
+    p.add_argument("--dir", help="Place links in a subdirectory")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
diff --git a/jcvi/apps/uclust.py b/jcvi/apps/uclust.py
index 0d0c3f73..76b9d040 100644
--- a/jcvi/apps/uclust.py
+++ b/jcvi/apps/uclust.py
@@ -240,10 +240,10 @@ def stats(args):
 
 
 def add_consensus_options(p):
-    p.add_option("--prefix", default="mcluster", help="Output prefix")
-    p.add_option("--minlength", default=30, type=int, help="Min contig length")
-    p.add_option("--mindepth", default=3, type=int, help="Min depth for each stack")
-    p.add_option("--minsamp", default=3, type=int, help="Min number of samples")
+    p.add_argument("--prefix", default="mcluster", help="Output prefix")
+    p.add_argument("--minlength", default=30, type=int, help="Min contig length")
+    p.add_argument("--mindepth", default=3, type=int, help="Min depth for each stack")
+    p.add_argument("--minsamp", default=3, type=int, help="Min number of samples")
 
 
 def find_pctid(consensusfiles):
@@ -430,7 +430,7 @@ def mconsensus(args):
     Call consensus along the stacks from cross-sample clustering.
     """
     p = OptionParser(mconsensus.__doc__)
-    p.add_option(
+    p.add_argument(
         "--allele_counts",
         default="allele_counts",
         help="Directory to generate allele counts",
@@ -556,7 +556,9 @@ def consensus(args):
     errors according to error rate, calls consensus.
     """
     p = OptionParser(consensus.__doc__)
-    p.add_option("--ploidy", default=2, type=int, help="Number of haplotypes per locus")
+    p.add_argument(
+        "--ploidy", default=2, type=int, help="Number of haplotypes per locus"
+    )
     add_consensus_options(p)
     p.set_verbose()
     opts, args = p.parse_args(args)
diff --git a/jcvi/apps/uniprot.py b/jcvi/apps/uniprot.py
index b99c8064..0d610fb1 100644
--- a/jcvi/apps/uniprot.py
+++ b/jcvi/apps/uniprot.py
@@ -98,36 +98,36 @@ def fetch(args):
 
     p = OptionParser(fetch.__doc__)
 
-    p.add_option(
+    p.add_argument(
         "--format",
         default="tab",
         choices=valid_formats,
         help="download format",
     )
-    p.add_option(
+    p.add_argument(
         "--columns",
         default="entry name, protein names, genes,organism",
         help="columns to download, if --format is `tab` or `xls`",
     )
-    p.add_option(
+    p.add_argument(
         "--include",
         default=False,
         action="store_true",
         help="Include isoforms when --format is `fasta` or include `description` when --format is `rdf`.",
     )
-    p.add_option(
+    p.add_argument(
         "--limit",
         default=10,
         type=int,
         help="Max number of results to retrieve",
     )
-    p.add_option(
+    p.add_argument(
         "--offset",
         default=0,
         type=int,
         help="Offset of first result, used with --limit",
     )
-    p.add_option(
+    p.add_argument(
         "--skipcheck",
         default=False,
         action="store_true",
diff --git a/jcvi/apps/vecscreen.py b/jcvi/apps/vecscreen.py
index 9f194502..d4345270 100644
--- a/jcvi/apps/vecscreen.py
+++ b/jcvi/apps/vecscreen.py
@@ -47,7 +47,7 @@ def mask(args):
     perform FASTA tidy if requested.
     """
     p = OptionParser(mask.__doc__)
-    p.add_option(
+    p.add_argument(
         "--db",
         default=ECOLI_URL,
         help="Contaminant db other than Ecoli K12, will download if file starts with http://, https://, or ftp://",
@@ -90,13 +90,13 @@ def blast(args):
     on the vector/contaminant ranges.
     """
     p = OptionParser(blast.__doc__)
-    p.add_option(
+    p.add_argument(
         "--dist",
         default=100,
         type=int,
         help="Merge adjacent HSPs separated by",
     )
-    p.add_option("--db", help="Use a different database rather than UniVec_Core")
+    p.add_argument("--db", help="Use a different database rather than UniVec_Core")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
diff --git a/jcvi/assembly/allmaps.py b/jcvi/assembly/allmaps.py
index 501f2a9b..9eaa285e 100644
--- a/jcvi/assembly/allmaps.py
+++ b/jcvi/assembly/allmaps.py
@@ -1013,10 +1013,10 @@ def split(args):
     modified through --chunk option.
     """
     p = OptionParser(split.__doc__)
-    p.add_option(
+    p.add_argument(
         "--chunk", default=4, type=int, help="Split chunks of at least N markers"
     )
-    p.add_option(
+    p.add_argument(
         "--splitsingle",
         default=False,
         action="store_true",
@@ -1061,7 +1061,7 @@ def movie(args):
     specific pseudomolecule, for example `chr1`.
     """
     p = OptionParser(movie.__doc__)
-    p.add_option(
+    p.add_argument(
         "--gapsize",
         default=100,
         type=int,
@@ -1151,9 +1151,9 @@ def estimategaps(args):
     The AGP file `input.chr.agp` will be modified in-place.
     """
     p = OptionParser(estimategaps.__doc__)
-    p.add_option("--minsize", default=100, type=int, help="Minimum gap size")
-    p.add_option("--maxsize", default=500000, type=int, help="Maximum gap size")
-    p.add_option(
+    p.add_argument("--minsize", default=100, type=int, help="Minimum gap size")
+    p.add_argument("--maxsize", default=500000, type=int, help="Maximum gap size")
+    p.add_argument(
         "--links",
         default=10,
         type=int,
@@ -1233,7 +1233,7 @@ def merge(args):
     scaffold_759,81336,1,9.7
     """
     p = OptionParser(merge.__doc__)
-    p.add_option(
+    p.add_argument(
         "-w", "--weightsfile", default="weights.txt", help="Write weights to file"
     )
     p.set_outfile("out.bed")
@@ -1274,7 +1274,7 @@ def mergebed(args):
     Combine bed maps to bed format, adding the map name.
     """
     p = OptionParser(mergebed.__doc__)
-    p.add_option(
+    p.add_argument(
         "-w", "--weightsfile", default="weights.txt", help="Write weights to file"
     )
     p.set_outfile("out.bed")
@@ -1357,52 +1357,56 @@ def path(args):
     """
     oargs = args
     p = OptionParser(path.__doc__)
-    p.add_option("-b", "--bedfile", help=SUPPRESS)
-    p.add_option("-s", "--fastafile", help=SUPPRESS)
-    p.add_option(
+    p.add_argument("-b", "--bedfile", help=SUPPRESS)
+    p.add_argument("-s", "--fastafile", help=SUPPRESS)
+    p.add_argument(
         "-w", "--weightsfile", default="weights.txt", help="Use weights from file"
     )
-    p.add_option(
+    p.add_argument(
         "--compress",
         default=1e-6,
         type=float,
         help="Compress markers with distance <=",
     )
-    p.add_option(
+    p.add_argument(
         "--noremoveoutliers",
         default=False,
         action="store_true",
         help="Don't remove outlier markers",
     )
-    p.add_option(
+    p.add_argument(
         "--distance",
         default="rank",
         choices=distance_choices,
         help="Distance function when building initial consensus",
     )
-    p.add_option(
+    p.add_argument(
         "--linkage",
         default="double",
         choices=linkage_choices,
         help="Linkage function when building initial consensus",
     )
-    p.add_option(
+    p.add_argument(
         "--gapsize",
         default=100,
         type=int,
         help="Insert gaps of size between scaffolds",
     )
-    p.add_option("--seqid", help="Only run partition with this seqid")
-    p.add_option("--partitions", help="Use predefined partitions of LGs")
-    p.add_option("--links", default=10, type=int, help="Only plot matchings more than")
-    p.add_option("--mincount", default=1, type=int, help="Minimum markers on a contig")
-    p.add_option(
+    p.add_argument("--seqid", help="Only run partition with this seqid")
+    p.add_argument("--partitions", help="Use predefined partitions of LGs")
+    p.add_argument(
+        "--links", default=10, type=int, help="Only plot matchings more than"
+    )
+    p.add_argument(
+        "--mincount", default=1, type=int, help="Minimum markers on a contig"
+    )
+    p.add_argument(
         "--noplot",
         default=False,
         action="store_true",
         help="Do not visualize the alignments",
     )
-    p.add_option(
+    p.add_argument(
         "--renumber",
         default=False,
         action="store_true",
@@ -1411,13 +1415,13 @@ def path(args):
     p.set_cpus(cpus=16)
 
     q = p.add_argument_group("Genetic algorithm options")
-    q.add_option(
+    q.add_argument(
         "--ngen", default=500, type=int, help="Iterations in GA, higher ~ slower"
     )
-    q.add_option(
+    q.add_argument(
         "--npop", default=100, type=int, help="Population size in GA, higher ~ slower"
     )
-    q.add_option("--seed", default=666, type=int, help="Random seed number")
+    q.add_argument("--seed", default=666, type=int, help="Random seed number")
     opts, args, iopts = p.set_image_options(args, figsize="10x6")
 
     if len(args) != 2:
@@ -1705,7 +1709,7 @@ def build(args):
     new positions of the markers will be reported in *.lifted.bed.
     """
     p = OptionParser(build.__doc__)
-    p.add_option(
+    p.add_argument(
         "--cleanup",
         default=False,
         action="store_true",
@@ -1768,17 +1772,19 @@ def build(args):
 
 
 def add_allmaps_plot_options(p):
-    p.add_option(
+    p.add_argument(
         "-w", "--weightsfile", default="weights.txt", help="Use weights from file"
     )
-    p.add_option(
+    p.add_argument(
         "--distance",
         default="cM",
         choices=distance_choices,
         help="Plot markers based on distance",
     )
-    p.add_option("--links", default=10, type=int, help="Only plot matchings more than")
-    p.add_option(
+    p.add_argument(
+        "--links", default=10, type=int, help="Only plot matchings more than"
+    )
+    p.add_argument(
         "--panels", default=False, action="store_true", help="Add panel labels A/B"
     )
 
@@ -1804,7 +1810,7 @@ def plot(args):
     from ..graphics.chromosome import Chromosome, GeneticMap, HorizontalChromosome
 
     p = OptionParser(plot.__doc__)
-    p.add_option("--title", help="Title of the plot")
+    p.add_argument("--title", help="Title of the plot")
     add_allmaps_plot_options(p)
     opts, args, iopts = p.set_image_options(args, figsize="10x6")
 
diff --git a/jcvi/assembly/allpaths.py b/jcvi/assembly/allpaths.py
index 1f172219..afa7ff8c 100644
--- a/jcvi/assembly/allpaths.py
+++ b/jcvi/assembly/allpaths.py
@@ -130,8 +130,8 @@ def dump(args):
     run allpaths folder.
     """
     p = OptionParser(dump.__doc__)
-    p.add_option("--dir", help="Working directory")
-    p.add_option(
+    p.add_argument("--dir", help="Working directory")
+    p.add_argument(
         "--nosim",
         default=False,
         action="store_true",
@@ -229,7 +229,7 @@ def fill(args):
     Run FillFragments on `frag_reads_corr.fastb`.
     """
     p = OptionParser(fill.__doc__)
-    p.add_option(
+    p.add_argument(
         "--stretch",
         default=3,
         type=int,
@@ -334,13 +334,13 @@ def pairs(args):
     from jcvi.assembly.preprocess import run_FastbAndQualb2Fastq
 
     p = OptionParser(pairs.__doc__)
-    p.add_option(
+    p.add_argument(
         "--header",
         default=False,
         action="store_true",
         help="Print header only",
     )
-    p.add_option(
+    p.add_argument(
         "--suffix",
         default=False,
         action="store_true",
@@ -415,19 +415,19 @@ def prepare(args):
     from jcvi.formats.fastq import guessoffset, readlen
 
     p = OptionParser(prepare.__doc__ + FastqNamings)
-    p.add_option(
+    p.add_argument(
         "--corr",
         default=False,
         action="store_true",
         help="Extra parameters for corrected data",
     )
-    p.add_option(
+    p.add_argument(
         "--norun",
         default=False,
         action="store_true",
         help="Don't write `run.sh` script",
     )
-    p.add_option("--ploidy", default="2", choices=("1", "2"), help="Ploidy")
+    p.add_argument("--ploidy", default="2", choices=("1", "2"), help="Ploidy")
     p.set_cpus()
     opts, args = p.parse_args(args)
 
diff --git a/jcvi/assembly/automaton.py b/jcvi/assembly/automaton.py
index 46074f69..b1c232ec 100644
--- a/jcvi/assembly/automaton.py
+++ b/jcvi/assembly/automaton.py
@@ -144,7 +144,7 @@ def contamination(args):
     from jcvi.apps.bowtie import align
 
     p = OptionParser(contamination.__doc__)
-    p.add_option(
+    p.add_argument(
         "--mapped",
         default=False,
         action="store_true",
@@ -235,7 +235,7 @@ def allpaths(args):
     Run automated ALLPATHS on list of dirs.
     """
     p = OptionParser(allpaths.__doc__)
-    p.add_option("--ploidy", default="1", choices=("1", "2"), help="Ploidy")
+    p.add_argument("--ploidy", default="1", choices=("1", "2"), help="Ploidy")
     opts, args = p.parse_args(args)
 
     if len(args) == 0:
@@ -263,7 +263,7 @@ def prepare(args):
     Note that JIRA report can also be a list of FASTQ files.
     """
     p = OptionParser(prepare.__doc__)
-    p.add_option(
+    p.add_argument(
         "--first",
         default=0,
         type=int,
diff --git a/jcvi/assembly/base.py b/jcvi/assembly/base.py
index 73189625..609acb6b 100644
--- a/jcvi/assembly/base.py
+++ b/jcvi/assembly/base.py
@@ -156,7 +156,7 @@ def n50(args):
     from jcvi.graphics.histogram import loghistogram
 
     p = OptionParser(n50.__doc__)
-    p.add_option(
+    p.add_argument(
         "--print0",
         default=False,
         action="store_true",
diff --git a/jcvi/assembly/gaps.py b/jcvi/assembly/gaps.py
index a975eeaa..4f50c3e5 100644
--- a/jcvi/assembly/gaps.py
+++ b/jcvi/assembly/gaps.py
@@ -38,7 +38,7 @@ def annotate(args):
     from jcvi.formats.agp import AGP, bed, tidy
 
     p = OptionParser(annotate.__doc__)
-    p.add_option("--minsize", default=200, help="Smallest component size")
+    p.add_argument("--minsize", default=200, help="Smallest component size")
     opts, args = p.parse_args(args)
 
     if len(args) != 3:
@@ -243,7 +243,7 @@ def flanks(args):
     Create sequences flanking the gaps.
     """
     p = OptionParser(flanks.__doc__)
-    p.add_option(
+    p.add_argument(
         "--extend",
         default=2000,
         type=int,
diff --git a/jcvi/assembly/geneticmap.py b/jcvi/assembly/geneticmap.py
index af86dcda..4d91c2b1 100644
--- a/jcvi/assembly/geneticmap.py
+++ b/jcvi/assembly/geneticmap.py
@@ -433,7 +433,7 @@ def heatmap(args):
     Calculate pairwise linkage disequilibrium given MSTmap.
     """
     p = OptionParser(heatmap.__doc__)
-    p.add_option(
+    p.add_argument(
         "--subsample",
         default=1000,
         type=int,
@@ -469,8 +469,8 @@ def header(args):
     from jcvi.formats.base import DictFile
 
     p = OptionParser(header.__doc__)
-    p.add_option("--prefix", default="", help="Prepend text to line number")
-    p.add_option("--ids", help="Write ids to file")
+    p.add_argument("--prefix", default="", help="Prepend text to line number")
+    p.add_argument("--ids", help="Write ids to file")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -570,13 +570,13 @@ def bed(args):
     Convert MSTMAP output into bed format.
     """
     p = OptionParser(bed.__doc__)
-    p.add_option(
+    p.add_argument(
         "--switch",
         default=False,
         action="store_true",
         help="Switch reference and aligned map elements",
     )
-    p.add_option(
+    p.add_argument(
         "--sep",
         default=".",
         help="Separator that is used to delimit scaffold and position in the marker name",
@@ -604,7 +604,7 @@ def fasta(args):
     from jcvi.formats.sizes import Sizes
 
     p = OptionParser(fasta.__doc__)
-    p.add_option(
+    p.add_argument(
         "--extend",
         default=1000,
         type=int,
@@ -673,7 +673,7 @@ def breakpoint(args):
     from more_itertools import pairwise
 
     p = OptionParser(breakpoint.__doc__)
-    p.add_option(
+    p.add_argument(
         "--diff",
         default=0.1,
         type=float,
diff --git a/jcvi/assembly/goldenpath.py b/jcvi/assembly/goldenpath.py
index fe3d47fe..4d81d82c 100644
--- a/jcvi/assembly/goldenpath.py
+++ b/jcvi/assembly/goldenpath.py
@@ -656,7 +656,7 @@ def anneal(args):
     """
     p = OptionParser(anneal.__doc__)
     p.set_align(pctid=GoodPct, hitlen=GoodOverlap)
-    p.add_option(
+    p.add_argument(
         "--hang", default=GoodOverhang, type=int, help="Maximum overhang length"
     )
     p.set_outdir(outdir="outdir")
@@ -759,7 +759,7 @@ def blast(args):
     from jcvi.apps.align import run_megablast
 
     p = OptionParser(blast.__doc__)
-    p.add_option("-n", type=int, default=2, help="Take best N hits")
+    p.add_argument("-n", type=int, default=2, help="Take best N hits")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -926,23 +926,23 @@ def overlap(args):
     from jcvi.formats.blast import chain_HSPs
 
     p = OptionParser(overlap.__doc__)
-    p.add_option(
+    p.add_argument(
         "--dir",
         default=os.getcwd(),
         help="Download sequences to dir",
     )
-    p.add_option(
+    p.add_argument(
         "--suffix",
         default="fasta",
         help="Suffix of the sequence file in dir",
     )
-    p.add_option(
+    p.add_argument(
         "--qreverse",
         default=False,
         action="store_true",
         help="Reverse seq a",
     )
-    p.add_option(
+    p.add_argument(
         "--nochain",
         default=False,
         action="store_true",
diff --git a/jcvi/assembly/hic.py b/jcvi/assembly/hic.py
index 6f68df86..90a3fd72 100644
--- a/jcvi/assembly/hic.py
+++ b/jcvi/assembly/hic.py
@@ -624,9 +624,9 @@ def dist(args):
     from jcvi.graphics.base import human_base_formatter, markup
 
     p = OptionParser(dist.__doc__)
-    p.add_option("--title", help="Title of the histogram")
-    p.add_option("--xmin", default=300, help="Minimum distance")
-    p.add_option("--xmax", default=6000000, help="Maximum distance")
+    p.add_argument("--title", help="Title of the histogram")
+    p.add_argument("--xmin", default=300, help="Minimum distance")
+    p.add_argument("--xmax", default=6000000, help="Maximum distance")
     opts, args, iopts = p.set_image_options(args, figsize="6x6")
 
     if len(args) != 2:
@@ -817,12 +817,12 @@ def heatmap(args):
     and seq2 individually with green color.
     """
     p = OptionParser(heatmap.__doc__)
-    p.add_option("--title", help="Title of the heatmap")
-    p.add_option("--groups", help="Groups file, see doc")
-    p.add_option("--vmin", default=1, type=int, help="Minimum value in the heatmap")
-    p.add_option("--vmax", default=6, type=int, help="Maximum value in the heatmap")
-    p.add_option("--chr", help="Plot this contig/chr only")
-    p.add_option(
+    p.add_argument("--title", help="Title of the heatmap")
+    p.add_argument("--groups", help="Groups file, see doc")
+    p.add_argument("--vmin", default=1, type=int, help="Minimum value in the heatmap")
+    p.add_argument("--vmax", default=6, type=int, help="Maximum value in the heatmap")
+    p.add_argument("--chr", help="Plot this contig/chr only")
+    p.add_argument(
         "--nobreaks",
         default=False,
         action="store_true",
@@ -935,13 +935,13 @@ def bam2mat(args):
     from jcvi.utils.cbook import percentage
 
     p = OptionParser(bam2mat.__doc__)
-    p.add_option(
+    p.add_argument(
         "--resolution",
         default=500000,
         type=int,
         help="Resolution when counting the links",
     )
-    p.add_option(
+    p.add_argument(
         "--seqids",
         default=None,
         help="Use a given seqids file, a single line with seqids joined by comma",
@@ -1063,10 +1063,10 @@ def simulate(args):
     - Genes are distributed uniformly
     """
     p = OptionParser(simulate.__doc__)
-    p.add_option("--genomesize", default=10000000, type=int, help="Genome size")
-    p.add_option("--genes", default=1000, type=int, help="Number of genes")
-    p.add_option("--contigs", default=100, type=int, help="Number of contigs")
-    p.add_option("--coverage", default=10, type=int, help="Link coverage")
+    p.add_argument("--genomesize", default=10000000, type=int, help="Genome size")
+    p.add_argument("--genes", default=1000, type=int, help="Number of genes")
+    p.add_argument("--contigs", default=100, type=int, help="Number of contigs")
+    p.add_argument("--coverage", default=10, type=int, help="Link coverage")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -1220,7 +1220,7 @@ def density(args):
     Estimate link density of contigs.
     """
     p = OptionParser(density.__doc__)
-    p.add_option(
+    p.add_argument(
         "--save",
         default=False,
         action="store_true",
@@ -1260,19 +1260,19 @@ def optimize(args):
     Optimize the contig order and orientation, based on CLM file.
     """
     p = OptionParser(optimize.__doc__)
-    p.add_option(
+    p.add_argument(
         "--skiprecover",
         default=False,
         action="store_true",
         help="Do not import 'recover' contigs",
     )
-    p.add_option(
+    p.add_argument(
         "--startover",
         default=False,
         action="store_true",
         help="Do not resume from existing tour file",
     )
-    p.add_option("--skipGA", default=False, action="store_true", help="Skip GA step")
+    p.add_argument("--skipGA", default=False, action="store_true", help="Skip GA step")
     p.set_outfile(outfile=None)
     p.set_cpus()
     opts, args = p.parse_args(args)
@@ -1479,8 +1479,8 @@ def movie(args):
     Plot optimization history.
     """
     p = OptionParser(movie.__doc__)
-    p.add_option("--frames", default=500, type=int, help="Only plot every N frames")
-    p.add_option(
+    p.add_argument("--frames", default=500, type=int, help="Only plot every N frames")
+    p.add_argument(
         "--engine",
         default="ffmpeg",
         choices=("ffmpeg", "gifsicle"),
@@ -1666,7 +1666,7 @@ def movieframe(args):
     Draw heatmap and synteny in the same plot.
     """
     p = OptionParser(movieframe.__doc__)
-    p.add_option("--label", help="Figure title")
+    p.add_argument("--label", help="Figure title")
     p.set_beds()
     p.set_outfile(outfile=None)
     opts, args, iopts = p.set_image_options(
diff --git a/jcvi/assembly/kmer.py b/jcvi/assembly/kmer.py
index 2f86b3ee..cb12ed39 100644
--- a/jcvi/assembly/kmer.py
+++ b/jcvi/assembly/kmer.py
@@ -624,7 +624,7 @@ def entropy(args):
     AAAAAAAAAAAGAAGAAAGAAA  34
     """
     p = OptionParser(entropy.__doc__)
-    p.add_option(
+    p.add_argument(
         "--threshold", default=0, type=int, help="Complexity needs to be above"
     )
     opts, args = p.parse_args(args)
@@ -684,38 +684,38 @@ def kmcop(args):
     Intersect or union kmc indices.
     """
     p = OptionParser(kmcop.__doc__)
-    p.add_option(
+    p.add_argument(
         "--action",
         choices=("union", "intersect", "reduce"),
         default="union",
         help="Action",
     )
-    p.add_option(
+    p.add_argument(
         "--ci_in",
         default=0,
         type=int,
         help="Exclude input kmers with less than ci_in counts",
     )
-    p.add_option(
+    p.add_argument(
         "--cs",
         default=0,
         type=int,
         help="Maximal value of a counter, only used when action is reduce",
     )
-    p.add_option(
+    p.add_argument(
         "--ci_out",
         default=0,
         type=int,
         help="Exclude output kmers with less than ci_out counts",
     )
-    p.add_option(
+    p.add_argument(
         "--batch",
         default=1,
         type=int,
         help="Number of batch, useful to reduce memory usage",
     )
-    p.add_option("--exclude", help="Exclude accessions from this list")
-    p.add_option("-o", default="results", help="Output name")
+    p.add_argument("--exclude", help="Exclude accessions from this list")
+    p.add_argument("-o", default="results", help="Output name")
     opts, args = p.parse_args(args)
 
     if len(args) < 2:
@@ -772,25 +772,25 @@ def kmc(args):
     Run kmc3 on Illumina reads.
     """
     p = OptionParser(kmc.__doc__)
-    p.add_option("-k", default=27, type=int, help="Kmer size")
-    p.add_option(
+    p.add_argument("-k", default=27, type=int, help="Kmer size")
+    p.add_argument(
         "--ci", default=2, type=int, help="Exclude kmers with less than ci counts"
     )
-    p.add_option("--cs", default=0, type=int, help="Maximal value of a counter")
-    p.add_option("--cx", type=int, help="Exclude kmers with more than cx counts")
-    p.add_option(
+    p.add_argument("--cs", default=0, type=int, help="Maximal value of a counter")
+    p.add_argument("--cx", type=int, help="Exclude kmers with more than cx counts")
+    p.add_argument(
         "--single",
         default=False,
         action="store_true",
         help="Input is single-end data, only one FASTQ/FASTA",
     )
-    p.add_option(
+    p.add_argument(
         "--fasta",
         default=False,
         action="store_true",
         help="Input is FASTA instead of FASTQ",
     )
-    p.add_option(
+    p.add_argument(
         "--mem", default=48, type=int, help="Max amount of RAM in GB (`kmc -m`)"
     )
     p.set_cpus()
@@ -838,7 +838,7 @@ def meryl(args):
     Run meryl on Illumina reads.
     """
     p = OptionParser(meryl.__doc__)
-    p.add_option("-k", default=19, type=int, help="Kmer size")
+    p.add_argument("-k", default=19, type=int, help="Kmer size")
     p.set_cpus()
     opts, args = p.parse_args(args)
 
@@ -879,8 +879,8 @@ def model(args):
     from scipy.stats import binom, poisson
 
     p = OptionParser(model.__doc__)
-    p.add_option("-k", default=23, type=int, help="Kmer size")
-    p.add_option("--cov", default=50, type=int, help="Expected coverage")
+    p.add_argument("-k", default=23, type=int, help="Kmer size")
+    p.add_argument("--cov", default=50, type=int, help="Expected coverage")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -1010,7 +1010,7 @@ def bincount(args):
     from jcvi.formats.sizes import Sizes
 
     p = OptionParser(bincount.__doc__)
-    p.add_option("-K", default=23, type=int, help="K-mer size")
+    p.add_argument("-K", default=23, type=int, help="K-mer size")
     p.set_outfile()
     opts, args = p.parse_args(args)
 
@@ -1073,7 +1073,7 @@ def dump(args):
     Convert FASTA sequences to list of K-mers.
     """
     p = OptionParser(dump.__doc__)
-    p.add_option("-K", default=23, type=int, help="K-mer size")
+    p.add_argument("-K", default=23, type=int, help="K-mer size")
     p.set_outfile()
     opts, args = p.parse_args(args)
 
@@ -1100,15 +1100,15 @@ def jellyfish(args):
     from jcvi.utils.cbook import human_size
 
     p = OptionParser(jellyfish.__doc__)
-    p.add_option("-K", default=23, type=int, help="K-mer size")
-    p.add_option(
+    p.add_argument("-K", default=23, type=int, help="K-mer size")
+    p.add_argument(
         "--coverage",
         default=40,
         type=int,
         help="Expected sequence coverage",
     )
-    p.add_option("--prefix", default="jf", help="Database prefix")
-    p.add_option(
+    p.add_argument("--prefix", default="jf", help="Database prefix")
+    p.add_argument(
         "--nohist",
         default=False,
         action="store_true",
@@ -1171,10 +1171,10 @@ def multihistogram(args):
     on Star et al.'s method (Atlantic Cod genome paper).
     """
     p = OptionParser(multihistogram.__doc__)
-    p.add_option("--kmin", default=15, type=int, help="Minimum K-mer size, inclusive")
-    p.add_option("--kmax", default=30, type=int, help="Maximum K-mer size, inclusive")
-    p.add_option("--vmin", default=2, type=int, help="Minimum value, inclusive")
-    p.add_option("--vmax", default=100, type=int, help="Maximum value, inclusive")
+    p.add_argument("--kmin", default=15, type=int, help="Minimum K-mer size, inclusive")
+    p.add_argument("--kmax", default=30, type=int, help="Maximum K-mer size, inclusive")
+    p.add_argument("--vmin", default=2, type=int, help="Minimum value, inclusive")
+    p.add_argument("--vmax", default=100, type=int, help="Maximum value, inclusive")
     opts, args, iopts = p.set_image_options(args, figsize="10x5", dpi=300)
 
     if len(args) < 1:
@@ -1349,37 +1349,37 @@ def histogram(args):
     only used to annotate the graphic.
     """
     p = OptionParser(histogram.__doc__)
-    p.add_option(
+    p.add_argument(
         "--vmin",
         dest="vmin",
         default=2,
         type=int,
         help="minimum value, inclusive",
     )
-    p.add_option(
+    p.add_argument(
         "--vmax",
         dest="vmax",
         default=200,
         type=int,
         help="maximum value, inclusive",
     )
-    p.add_option(
+    p.add_argument(
         "--method",
         choices=("nbinom", "allpaths"),
         default="nbinom",
         help="'nbinom' - slow but more accurate for het or polyploid genome; "
         + "'allpaths' - fast and works for homozygous enomes",
     )
-    p.add_option(
+    p.add_argument(
         "--maxiter",
         default=100,
         type=int,
         help="Max iterations for optimization. Only used with --method nbinom",
     )
-    p.add_option(
+    p.add_argument(
         "--coverage", default=0, type=int, help="Kmer coverage [default: auto]"
     )
-    p.add_option(
+    p.add_argument(
         "--nopeaks",
         default=False,
         action="store_true",
diff --git a/jcvi/assembly/opticalmap.py b/jcvi/assembly/opticalmap.py
index 249ebf94..8ac22739 100644
--- a/jcvi/assembly/opticalmap.py
+++ b/jcvi/assembly/opticalmap.py
@@ -380,26 +380,26 @@ def bed(args):
     from jcvi.formats.bed import sort
 
     p = OptionParser(bed.__doc__)
-    p.add_option(
+    p.add_argument(
         "--blockonly",
         default=False,
         action="store_true",
         help="Only print out large blocks, not fragments",
     )
-    p.add_option(
+    p.add_argument(
         "--point",
         default=False,
         action="store_true",
         help="Print accesssion as single point instead of interval",
     )
-    p.add_option("--scale", type=float, help="Scale the OM distance by factor")
-    p.add_option(
+    p.add_argument("--scale", type=float, help="Scale the OM distance by factor")
+    p.add_argument(
         "--switch",
         default=False,
         action="store_true",
         help="Switch reference and aligned map elements",
     )
-    p.add_option(
+    p.add_argument(
         "--nosort",
         default=False,
         action="store_true",
diff --git a/jcvi/assembly/patch.py b/jcvi/assembly/patch.py
index 02b8505e..8735c9ae 100644
--- a/jcvi/assembly/patch.py
+++ b/jcvi/assembly/patch.py
@@ -83,19 +83,19 @@ def pastegenes(args):
     from jcvi.utils.cbook import gene_name
 
     p = OptionParser(pastegenes.__doc__)
-    p.add_option(
+    p.add_argument(
         "--cutoff",
         default=90,
         type=int,
         help="Coverage cutoff to call gene missing",
     )
-    p.add_option(
+    p.add_argument(
         "--flank",
         default=2000,
         type=int,
         help="Get the seq of size on two ends",
     )
-    p.add_option(
+    p.add_argument(
         "--maxsize",
         default=50000,
         type=int,
@@ -200,7 +200,7 @@ def pasteprepare(args):
     Prepare sequences for paste.
     """
     p = OptionParser(pasteprepare.__doc__)
-    p.add_option(
+    p.add_argument(
         "--flank",
         default=5000,
         type=int,
@@ -238,13 +238,13 @@ def paste(args):
     from jcvi.formats.bed import uniq
 
     p = OptionParser(paste.__doc__)
-    p.add_option(
+    p.add_argument(
         "--maxsize",
         default=300000,
         type=int,
         help="Maximum size of patchers to be replaced",
     )
-    p.add_option("--prefix", help="Prefix of the new object")
+    p.add_argument("--prefix", help="Prefix of the new object")
     p.set_rclip(rclip=1)
     opts, args = p.parse_args(args)
 
@@ -298,7 +298,7 @@ def closest(args):
     Identify the nearest gaps flanking suggested regions.
     """
     p = OptionParser(closest.__doc__)
-    p.add_option(
+    p.add_argument(
         "--om",
         default=False,
         action="store_true",
@@ -516,7 +516,7 @@ def fill(args):
     Perform gap filling of one assembly (bad) using sequences from another.
     """
     p = OptionParser(fill.__doc__)
-    p.add_option(
+    p.add_argument(
         "--extend",
         default=2000,
         type=int,
@@ -730,14 +730,14 @@ def install(args):
 
     p = OptionParser(install.__doc__)
     p.set_rclip(rclip=1)
-    p.add_option(
+    p.add_argument(
         "--maxsize",
         default=300000,
         type=int,
         help="Maximum size of patchers to be replaced",
     )
-    p.add_option("--prefix", help="Prefix of the new object")
-    p.add_option(
+    p.add_argument("--prefix", help="Prefix of the new object")
+    p.add_argument(
         "--strict",
         default=False,
         action="store_true",
@@ -814,7 +814,7 @@ def refine(args):
     from pybedtools import BedTool
 
     p = OptionParser(refine.__doc__)
-    p.add_option(
+    p.add_argument(
         "--closest",
         default=False,
         action="store_true",
@@ -917,12 +917,12 @@ def patcher(args):
     from jcvi.formats.bed import uniq
 
     p = OptionParser(patcher.__doc__)
-    p.add_option(
+    p.add_argument(
         "--backbone",
         default="OM",
         help="Prefix of the backbone assembly",
     )
-    p.add_option("--object", default="object", help="New object name")
+    p.add_argument("--object", default="object", help="New object name")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
diff --git a/jcvi/assembly/postprocess.py b/jcvi/assembly/postprocess.py
index 42cf4395..13737762 100644
--- a/jcvi/assembly/postprocess.py
+++ b/jcvi/assembly/postprocess.py
@@ -126,7 +126,7 @@ def circular(args):
     from jcvi.assembly.goldenpath import overlap
 
     p = OptionParser(circular.__doc__)
-    p.add_option(
+    p.add_argument(
         "--flip",
         default=False,
         action="store_true",
@@ -246,7 +246,7 @@ def build(args):
     from jcvi.formats.fasta import sort
 
     p = OptionParser(build.__doc__)
-    p.add_option(
+    p.add_argument(
         "--nodedup",
         default=False,
         action="store_true",
@@ -283,7 +283,7 @@ def screen(args):
 
     p = OptionParser(screen.__doc__)
     p.set_align(pctid=95, pctcov=50)
-    p.add_option("--best", default=1, type=int, help="Get the best N hit")
+    p.add_argument("--best", default=1, type=int, help="Get the best N hit")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -324,7 +324,7 @@ def scaffold(args):
     from jcvi.formats.bed import Bed
 
     p = OptionParser(scaffold.__doc__)
-    p.add_option(
+    p.add_argument(
         "--prefix",
         default=False,
         action="store_true",
diff --git a/jcvi/assembly/preprocess.py b/jcvi/assembly/preprocess.py
index c8344571..d11b6b9c 100644
--- a/jcvi/assembly/preprocess.py
+++ b/jcvi/assembly/preprocess.py
@@ -100,11 +100,11 @@ def diginorm(args):
     from jcvi.apps.base import getfilesize
 
     p = OptionParser(diginorm.__doc__)
-    p.add_option(
+    p.add_argument(
         "--single", default=False, action="store_true", help="Single end reads"
     )
-    p.add_option("--tablesize", help="Memory size")
-    p.add_option(
+    p.add_argument("--tablesize", help="Memory size")
+    p.add_argument(
         "--npass",
         default="1",
         choices=("1", "2"),
@@ -309,8 +309,8 @@ def count(args):
     from jcvi.utils.table import loadtable, write_csv
 
     p = OptionParser(count.__doc__)
-    p.add_option("--dir", help="Sub-directory where FASTQC was run")
-    p.add_option(
+    p.add_argument("--dir", help="Sub-directory where FASTQC was run")
+    p.add_argument(
         "--human",
         default=False,
         action="store_true",
@@ -353,9 +353,9 @@ def hetsmooth(args):
                reads_1.fq reads_2.fq
     """
     p = OptionParser(hetsmooth.__doc__)
-    p.add_option("-K", default=23, type=int, help="K-mer size")
-    p.add_option("-L", type=int, help="Bottom threshold, first min")
-    p.add_option("-U", type=int, help="Top threshold, second min")
+    p.add_argument("-K", default=23, type=int, help="K-mer size")
+    p.add_argument("-L", type=int, help="Bottom threshold, first min")
+    p.add_argument("-U", type=int, help="Top threshold, second min")
     opts, args = p.parse_args(args)
 
     if len(args) != 3:
@@ -389,43 +389,43 @@ def trim(args):
     tv = "0.32"
     TrimJar = "trimmomatic-{0}.jar".format(tv)
     p = OptionParser(trim.__doc__)
-    p.add_option(
+    p.add_argument(
         "--path",
         default=op.join("~/bin", TrimJar),
         help="Path to trimmomatic jar file",
     )
     p.set_phred()
-    p.add_option(
+    p.add_argument(
         "--nofrags",
         default=False,
         action="store_true",
         help="Discard frags file in PE mode",
     )
-    p.add_option(
+    p.add_argument(
         "--minqv",
         default=15,
         type=int,
         help="Average qv after trimming",
     )
-    p.add_option(
+    p.add_argument(
         "--minlen",
         default=36,
         type=int,
         help="Minimum length after trimming",
     )
-    p.add_option(
+    p.add_argument(
         "--adapteronly",
         default=False,
         action="store_true",
         help="Only trim adapters with no qv trimming",
     )
-    p.add_option(
+    p.add_argument(
         "--nogz",
         default=False,
         action="store_true",
         help="Do not write to gzipped files",
     )
-    p.add_option(
+    p.add_argument(
         "--log",
         default=None,
         dest="trimlog",
@@ -583,21 +583,21 @@ def correct(args):
     from jcvi.assembly.base import FastqNamings
 
     p = OptionParser(correct.__doc__ + FastqNamings)
-    p.add_option("--dir", default="data", help="Working directory")
-    p.add_option(
+    p.add_argument("--dir", default="data", help="Working directory")
+    p.add_argument(
         "--fragsdedup",
         default=False,
         action="store_true",
         help="Don't deduplicate the fragment reads",
     )
-    p.add_option("--ploidy", default="2", choices=("1", "2"), help="Ploidy")
-    p.add_option(
+    p.add_argument("--ploidy", default="2", choices=("1", "2"), help="Ploidy")
+    p.add_argument(
         "--haploidify",
         default=False,
         action="store_true",
         help="Set HAPLOIDIFY=True",
     )
-    p.add_option(
+    p.add_argument(
         "--suffix",
         default=False,
         action="store_true",
diff --git a/jcvi/assembly/sim.py b/jcvi/assembly/sim.py
index c9f7dad2..19b39f55 100644
--- a/jcvi/assembly/sim.py
+++ b/jcvi/assembly/sim.py
@@ -29,13 +29,13 @@ def add_sim_options(p):
     """
     Add options shared by eagle or wgsim.
     """
-    p.add_option(
+    p.add_argument(
         "--distance",
         default=500,
         type=int,
         help="Outer distance between the two ends",
     )
-    p.add_option("--readlen", default=150, type=int, help="Length of the read")
+    p.add_argument("--readlen", default=150, type=int, help="Length of the read")
     p.set_depth(depth=10)
     p.set_outfile(outfile=None)
 
@@ -46,7 +46,7 @@ def eagle(args):
 
     """
     p = OptionParser(eagle.__doc__)
-    p.add_option(
+    p.add_argument(
         "--share", default="/usr/local/share/EAGLE/", help="Default EAGLE share path"
     )
     add_sim_options(p)
@@ -158,19 +158,19 @@ def wgsim(args):
     Run dwgsim on fastafile.
     """
     p = OptionParser(wgsim.__doc__)
-    p.add_option(
+    p.add_argument(
         "--erate",
         default=0.01,
         type=float,
         help="Base error rate of the read",
     )
-    p.add_option(
+    p.add_argument(
         "--noerrors",
         default=False,
         action="store_true",
         help="Simulate reads with no errors",
     )
-    p.add_option(
+    p.add_argument(
         "--genomesize",
         type=int,
         help="Genome size in Mb [default: estimate from data]",
diff --git a/jcvi/assembly/soap.py b/jcvi/assembly/soap.py
index 90b2ba86..273370f8 100644
--- a/jcvi/assembly/soap.py
+++ b/jcvi/assembly/soap.py
@@ -135,8 +135,8 @@ def clean(args):
     Clean and dedup paired FASTQ files.
     """
     p = OptionParser(clean.__doc__)
-    p.add_option("-a", default=0, type=int, help="Trim length at 5' end")
-    p.add_option("-b", default=50, type=int, help="Trim length at 3' end")
+    p.add_argument("-a", default=0, type=int, help="Trim length at 5' end")
+    p.add_argument("-b", default=50, type=int, help="Trim length at 3' end")
     p.set_cpus()
     opts, args = p.parse_args(args)
 
@@ -233,15 +233,15 @@ def prepare(args):
     from jcvi.formats.base import write_file
 
     p = OptionParser(prepare.__doc__ + FastqNamings)
-    p.add_option("-K", default=45, type=int, help="K-mer size")
-    p.add_option(
+    p.add_argument("-K", default=45, type=int, help="K-mer size")
+    p.add_argument(
         "--assemble_1st_rank_only",
         default=False,
         action="store_true",
         help="Assemble the first rank only, other libs asm_flags=2",
     )
-    p.add_option("--scaffold", help="Only perform scaffolding")
-    p.add_option("--gapclose", help="Only perform gap closure")
+    p.add_argument("--scaffold", help="Only perform scaffolding")
+    p.add_argument("--gapclose", help="Only perform gap closure")
     p.set_cpus()
     opts, args = p.parse_args(args)
 
diff --git a/jcvi/assembly/syntenypath.py b/jcvi/assembly/syntenypath.py
index 94ca1e7d..c0b1e855 100644
--- a/jcvi/assembly/syntenypath.py
+++ b/jcvi/assembly/syntenypath.py
@@ -134,13 +134,15 @@ def bed(args):
     from ..compara.base import AnchorFile
 
     p = OptionParser(bed.__doc__)
-    p.add_option(
+    p.add_argument(
         "--switch",
         default=False,
         action="store_true",
         help="Switch reference and aligned map elements",
     )
-    p.add_option("--scale", type=float, help="Scale the aligned map distance by factor")
+    p.add_argument(
+        "--scale", type=float, help="Scale the aligned map distance by factor"
+    )
     p.set_beds()
     p.set_outfile()
     opts, args = p.parse_args(args)
@@ -228,14 +230,14 @@ def partition(args):
     """
     allowed_format = ("png", "ps")
     p = OptionParser(partition.__doc__)
-    p.add_option("--prefix", help="Add prefix to the name")
-    p.add_option(
+    p.add_argument("--prefix", help="Add prefix to the name")
+    p.add_argument(
         "--namestart",
         default=0,
         type=int,
         help="Use a shorter name, starting index",
     )
-    p.add_option(
+    p.add_argument(
         "--format",
         default="png",
         choices=allowed_format,
@@ -297,7 +299,7 @@ def merge(args):
     Merge multiple graphs together and visualize.
     """
     p = OptionParser(merge.__doc__)
-    p.add_option(
+    p.add_argument(
         "--colorlist",
         default="black,red,pink,blue,green",
         help="The color palette",
@@ -339,7 +341,7 @@ def happy(args):
     +-8254707:8254647:-8254690:{[8254694]:[8254713]:[8254531]:[8254797]}:8254802:8254788+
     """
     p = OptionParser(happy.__doc__)
-    p.add_option("--prefix", help="Add prefix to the name")
+    p.add_argument("--prefix", help="Add prefix to the name")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -374,13 +376,13 @@ def fromblast(args):
     from jcvi.utils.range import range_distance
 
     p = OptionParser(fromblast.__doc__)
-    p.add_option(
+    p.add_argument(
         "--clique",
         default=False,
         action="store_true",
         help="Populate clique instead of linear path",
     )
-    p.add_option(
+    p.add_argument(
         "--maxdist",
         default=100000,
         type=int,
@@ -484,7 +486,7 @@ def connect(args):
     Connect contigs using long reads.
     """
     p = OptionParser(connect.__doc__)
-    p.add_option(
+    p.add_argument(
         "--clip",
         default=2000,
         type=int,
diff --git a/jcvi/compara/blastfilter.py b/jcvi/compara/blastfilter.py
index 46fa2662..c44f4a68 100755
--- a/jcvi/compara/blastfilter.py
+++ b/jcvi/compara/blastfilter.py
@@ -290,20 +290,20 @@ def main(args):
     p = OptionParser(__doc__)
     p.set_beds()
     p.set_stripnames()
-    p.add_option(
+    p.add_argument(
         "--tandems_only",
         dest="tandems_only",
         action="store_true",
         default=False,
         help="only calculate tandems, write .localdup file and exit.",
     )
-    p.add_option(
+    p.add_argument(
         "--tandem_Nmax",
         type=int,
         default=10,
         help="merge tandem genes within distance",
     )
-    p.add_option(
+    p.add_argument(
         "--cscore",
         type=float,
         default=0.7,
@@ -311,7 +311,7 @@ def main(args):
         "keep all values that are 50% or greater of the best hit. "
         "higher is more stringent",
     )
-    p.add_option("--exclude", help="Remove anchors from a previous run")
+    p.add_argument("--exclude", help="Remove anchors from a previous run")
 
     opts, args = p.parse_args(args)
 
diff --git a/jcvi/compara/catalog.py b/jcvi/compara/catalog.py
index 1a455002..25d7444b 100644
--- a/jcvi/compara/catalog.py
+++ b/jcvi/compara/catalog.py
@@ -119,7 +119,7 @@ def enrich(args):
     Enrich OMG output by pulling genes misses by OMG.
     """
     p = OptionParser(enrich.__doc__)
-    p.add_option(
+    p.add_argument(
         "--ghost",
         default=False,
         action="store_true",
@@ -309,7 +309,7 @@ def layout(args):
     separated by comma in place of taxa, e.g. "BR,BO,AN,CN"
     """
     p = OptionParser(layout.__doc__)
-    p.add_option("--sort", help="Sort layout file based on bedfile")
+    p.add_argument("--sort", help="Sort layout file based on bedfile")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -508,9 +508,11 @@ def omgprepare(args):
     from jcvi.formats.base import DictFile
 
     p = OptionParser(omgprepare.__doc__)
-    p.add_option("--norbh", action="store_true", help="Disable RBH hits")
-    p.add_option("--pctid", default=0, type=int, help="Percent id cutoff for RBH hits")
-    p.add_option("--cscore", default=90, type=int, help="C-score cutoff for RBH hits")
+    p.add_argument("--norbh", action="store_true", help="Disable RBH hits")
+    p.add_argument(
+        "--pctid", default=0, type=int, help="Percent id cutoff for RBH hits"
+    )
+    p.add_argument("--cscore", default=90, type=int, help="C-score cutoff for RBH hits")
     p.set_stripnames()
     p.set_beds()
 
@@ -609,24 +611,24 @@ def ortholog(args):
     from jcvi.formats.blast import cscore, filter, filtered_blastfile_name
 
     p = OptionParser(ortholog.__doc__)
-    p.add_option(
+    p.add_argument(
         "--dbtype",
         default="nucl",
         choices=("nucl", "prot"),
         help="Molecule type of subject database",
     )
 
-    p.add_option(
+    p.add_argument(
         "--full",
         default=False,
         action="store_true",
         help="Run in full 1x1 mode, including blocks and RBH",
     )
-    p.add_option("--cscore", default=0.7, type=float, help="C-score cutoff")
-    p.add_option(
+    p.add_argument("--cscore", default=0.7, type=float, help="C-score cutoff")
+    p.add_argument(
         "--dist", default=20, type=int, help="Extent of flanking regions to search"
     )
-    p.add_option(
+    p.add_argument(
         "-n",
         "--min_size",
         dest="n",
@@ -634,41 +636,41 @@ def ortholog(args):
         default=4,
         help="minimum number of anchors in a cluster",
     )
-    p.add_option("--quota", help="Quota align parameter")
-    p.add_option("--exclude", help="Remove anchors from a previous run")
-    p.add_option(
+    p.add_argument("--quota", help="Quota align parameter")
+    p.add_argument("--exclude", help="Remove anchors from a previous run")
+    p.add_argument(
         "--self_remove",
         default=98,
         type=float,
         help="Remove self hits that are above this percent identity",
     )
-    p.add_option(
+    p.add_argument(
         "--no_strip_names",
         default=False,
         action="store_true",
         help="Do not strip alternative splicing (e.g. At5g06540.1 -> At5g06540)",
     )
-    p.add_option(
+    p.add_argument(
         "--liftover_dist",
         type=int,
         help="Distance to extend from liftover. Defaults to half of --dist",
     )
     p.set_cpus()
     dotplot_group = p.set_dotplot_opts()
-    dotplot_group.add_option(
+    dotplot_group.add_argument(
         "--notex", default=False, action="store_true", help="Do not use tex"
     )
-    dotplot_group.add_option(
+    dotplot_group.add_argument(
         "--no_dotplot", default=False, action="store_true", help="Do not make dotplot"
     )
-    p.add_option(
+    p.add_argument(
         "--ignore_zero_anchor",
         default=False,
         action="store_true",
         help="Ignore this pair of ortholog identification instead of throwing an error when performing many pairs of cataloging.",
     )
 
-    p.add_option(
+    p.add_argument(
         "--align_soft",
         default="last",
         choices=("last", "blast", "diamond_blastp"),
@@ -921,34 +923,34 @@ def tandem(args):
     pep_file can also be used in same manner.
     """
     p = OptionParser(tandem.__doc__)
-    p.add_option(
+    p.add_argument(
         "--tandem_Nmax",
         dest="tandem_Nmax",
         type=int,
         default=3,
         help="merge tandem genes within distance",
     )
-    p.add_option(
+    p.add_argument(
         "--percent_overlap",
         type=int,
         default=50,
         help="tandem genes have >=x% aligned sequence, x=0-100",
     )
     p.set_align(evalue=0.01)
-    p.add_option(
+    p.add_argument(
         "--not_self",
         default=False,
         action="store_true",
         help="provided is not self blast file",
     )
-    p.add_option(
+    p.add_argument(
         "--strip_gene_name",
         dest="sep",
         type=str,
         default=".",
         help="strip alternative splicing. Use None for no stripping.",
     )
-    p.add_option(
+    p.add_argument(
         "--genefamily",
         dest="genefam",
         action="store_true",
diff --git a/jcvi/compara/fractionation.py b/jcvi/compara/fractionation.py
index 24682677..7452702d 100644
--- a/jcvi/compara/fractionation.py
+++ b/jcvi/compara/fractionation.py
@@ -156,7 +156,7 @@ def segment(args):
     from jcvi.formats.base import SetFile
 
     p = OptionParser(segment.__doc__)
-    p.add_option(
+    p.add_argument(
         "--chain",
         default=1,
         type=int,
@@ -354,7 +354,7 @@ def gaps(args):
     from jcvi.utils.cbook import percentage
 
     p = OptionParser(gaps.__doc__)
-    p.add_option("--bdist", default=0, type=int, help="Base pair distance")
+    p.add_argument("--bdist", default=0, type=int, help="Base pair distance")
     opts, args = p.parse_args(args)
 
     if len(args) != 3:
@@ -439,7 +439,7 @@ def summary(args):
     from jcvi.utils.cbook import percentage, Registry
 
     p = OptionParser(summary.__doc__)
-    p.add_option("--extra", help="Cross with extra tsv file")
+    p.add_argument("--extra", help="Cross with extra tsv file")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -672,14 +672,14 @@ def loss(args):
     Extract likely gene loss candidates between genome a and b.
     """
     p = OptionParser(loss.__doc__)
-    p.add_option(
+    p.add_argument(
         "--bed",
         default=False,
         action="store_true",
         help="Genomic BLAST is in bed format",
     )
-    p.add_option("--gdist", default=20, type=int, help="Gene distance")
-    p.add_option(
+    p.add_argument("--gdist", default=20, type=int, help="Gene distance")
+    p.add_argument(
         "--bdist",
         default=20000,
         type=int,
diff --git a/jcvi/compara/ks.py b/jcvi/compara/ks.py
index 60aa5b89..53ddd533 100644
--- a/jcvi/compara/ks.py
+++ b/jcvi/compara/ks.py
@@ -364,7 +364,7 @@ def gc3(args):
     concatenated or separated.
     """
     p = OptionParser(gc3.__doc__)
-    p.add_option(
+    p.add_argument(
         "--plot", default=False, action="store_true", help="Also plot the GC3 histogram"
     )
     p.set_outfile()
@@ -549,18 +549,18 @@ def calc(args):
     from jcvi.formats.fasta import translate
 
     p = OptionParser(calc.__doc__)
-    p.add_option(
+    p.add_argument(
         "--longest",
         action="store_true",
         help="Get longest ORF, only works if no pep file, e.g. ESTs",
     )
-    p.add_option(
+    p.add_argument(
         "--msa",
         default="clustalw",
         choices=("clustalw", "muscle"),
         help="software used to align the proteins",
     )
-    p.add_option("--workdir", default=os.getcwd(), help="Work directory")
+    p.add_argument("--workdir", default=os.getcwd(), help="Work directory")
     p.set_outfile()
 
     opts, args = p.parse_args(args)
@@ -822,10 +822,10 @@ def subset(args):
     in tab delimited pairsfile/anchorfile.
     """
     p = OptionParser(subset.__doc__)
-    p.add_option(
+    p.add_argument(
         "--noheader", action="store_true", help="don't write ksfile header line"
     )
-    p.add_option(
+    p.add_argument(
         "--block", action="store_true", help="preserve block structure in input"
     )
     p.set_stripnames()
@@ -1081,21 +1081,25 @@ def plot_ks_dist(
 
 
 def add_plot_options(p):
-    p.add_option("--fit", default=False, action="store_true", help="Plot fitted lines")
-    p.add_option("--kde", default=False, action="store_true", help="Use KDE smoothing")
-    p.add_option("--vmin", default=0.0, type=float, help="Minimum value, inclusive")
-    p.add_option("--vmax", default=3.0, type=float, help="Maximum value, inclusive")
-    p.add_option(
+    p.add_argument(
+        "--fit", default=False, action="store_true", help="Plot fitted lines"
+    )
+    p.add_argument(
+        "--kde", default=False, action="store_true", help="Use KDE smoothing"
+    )
+    p.add_argument("--vmin", default=0.0, type=float, help="Minimum value, inclusive")
+    p.add_argument("--vmax", default=3.0, type=float, help="Maximum value, inclusive")
+    p.add_argument(
         "--bins", default=60, type=int, help="Number of bins to plot in the histogram"
     )
-    p.add_option("--legendp", default="upper right", help="Place of the legend")
-    p.add_option(
+    p.add_argument("--legendp", default="upper right", help="Place of the legend")
+    p.add_argument(
         "--fill",
         default=False,
         action="store_true",
         help="Do not fill the histogram area",
     )
-    p.add_option("--title", default="*Ks* distribution", help="Title of the plot")
+    p.add_argument("--title", default="*Ks* distribution", help="Title of the plot")
 
 
 def report(args):
@@ -1109,13 +1113,13 @@ def report(args):
     from jcvi.graphics.histogram import stem_leaf_plot
 
     p = OptionParser(report.__doc__)
-    p.add_option(
+    p.add_argument(
         "--pdf",
         default=False,
         action="store_true",
         help="Generate graphic output for the histogram",
     )
-    p.add_option(
+    p.add_argument(
         "--components",
         default=1,
         type=int,
diff --git a/jcvi/compara/pad.py b/jcvi/compara/pad.py
index e0b68edd..37e7988a 100644
--- a/jcvi/compara/pad.py
+++ b/jcvi/compara/pad.py
@@ -106,7 +106,7 @@ def pad(args):
 
     p = OptionParser(pad.__doc__)
     p.set_beds()
-    p.add_option(
+    p.add_argument(
         "--cutoff",
         default=0.3,
         type=float,
@@ -238,10 +238,10 @@ def cluster(args):
 
     p = OptionParser(cluster.__doc__)
     p.set_beds()
-    p.add_option(
+    p.add_argument(
         "--minsize", default=10, type=int, help="Only segment using blocks >= size"
     )
-    p.add_option(
+    p.add_argument(
         "--path", default="~/scratch/bin", help="Path to the CLUSTER 3.0 binary"
     )
 
diff --git a/jcvi/compara/pedigree.py b/jcvi/compara/pedigree.py
index 72ca2dab..94536fca 100644
--- a/jcvi/compara/pedigree.py
+++ b/jcvi/compara/pedigree.py
@@ -238,9 +238,9 @@ def pedigree(args):
     Plot pedigree and calculate pedigree coefficients from a pedigree file.
     """
     p = OptionParser(pedigree.__doc__)
-    p.add_option("--ploidy", default=2, type=int, help="Ploidy")
-    p.add_option("--N", default=10000, type=int, help="Number of samples")
-    p.add_option("--title", default="", help="Title of the graph")
+    p.add_argument("--ploidy", default=2, type=int, help="Ploidy")
+    p.add_argument("--N", default=10000, type=int, help="Number of samples")
+    p.add_argument("--title", default="", help="Title of the graph")
     opts, args, iopts = p.set_image_options(args)
 
     if len(args) != 1:
diff --git a/jcvi/compara/phylogeny.py b/jcvi/compara/phylogeny.py
index 859c4d08..0994460d 100644
--- a/jcvi/compara/phylogeny.py
+++ b/jcvi/compara/phylogeny.py
@@ -21,8 +21,10 @@ def lcn(args):
     %prog lcn Orthogroups/Orthogroups.tsv Orthogroup_Sequences/ lcn/
     """
     p = OptionParser(lcn.__doc__)
-    p.add_option("--min-single-ratio", default=0.9, help="Single copy ratio must be > ")
-    p.add_option("--max-zero-ratio", default=0, help="Zero copy ratio must be < ")
+    p.add_argument(
+        "--min-single-ratio", default=0.9, help="Single copy ratio must be > "
+    )
+    p.add_argument("--max-zero-ratio", default=0, help="Zero copy ratio must be < ")
     opts, args = p.parse_args(args)
 
     if len(args) != 3:
diff --git a/jcvi/compara/quota.py b/jcvi/compara/quota.py
index aa5a1d9a..9efbca08 100755
--- a/jcvi/compara/quota.py
+++ b/jcvi/compara/quota.py
@@ -186,7 +186,7 @@ def main(args):
     p = OptionParser(__doc__)
 
     p.set_beds()
-    p.add_option(
+    p.add_argument(
         "--quota",
         default="1:1",
         help="`quota mapping` procedure -- screen blocks to constrain mapping"
@@ -194,7 +194,7 @@ def main(args):
         "put in the format like (#subgenomes expected for genome X):"
         "(#subgenomes expected for genome Y)",
     )
-    p.add_option(
+    p.add_argument(
         "--Nm",
         dest="Nmax",
         type=int,
@@ -204,7 +204,7 @@ def main(args):
         "[default: %default units (gene or bp dist)]",
     )
 
-    p.add_option(
+    p.add_argument(
         "--self",
         dest="self_match",
         action="store_true",
@@ -214,7 +214,7 @@ def main(args):
     )
     p.set_verbose(help="Show verbose solver output")
 
-    p.add_option(
+    p.add_argument(
         "--screen",
         default=False,
         action="store_true",
diff --git a/jcvi/compara/reconstruct.py b/jcvi/compara/reconstruct.py
index 6ffb461e..ccb494f7 100644
--- a/jcvi/compara/reconstruct.py
+++ b/jcvi/compara/reconstruct.py
@@ -244,7 +244,7 @@ def zipbed(args):
     proceeds by interleaving the genes together.
     """
     p = OptionParser(zipbed.__doc__)
-    p.add_option("--prefix", default="b", help="Prefix for the new seqid")
+    p.add_argument("--prefix", default="b", help="Prefix for the new seqid")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
diff --git a/jcvi/compara/synfind.py b/jcvi/compara/synfind.py
index b413e477..96c826a3 100755
--- a/jcvi/compara/synfind.py
+++ b/jcvi/compara/synfind.py
@@ -248,22 +248,22 @@ def main(blastfile, p, opts):
     p.set_outfile()
 
     coge_group = p.add_argument_group("CoGe-specific options")
-    coge_group.add_option("--sqlite", help="Write sqlite database")
-    coge_group.add_option("--qnote", default="null", help="Query dataset group id")
-    coge_group.add_option("--snote", default="null", help="Subject dataset group id")
+    coge_group.add_argument("--sqlite", help="Write sqlite database")
+    coge_group.add_argument("--qnote", default="null", help="Query dataset group id")
+    coge_group.add_argument("--snote", default="null", help="Subject dataset group id")
 
     params_group = p.add_argument_group("Synteny parameters")
-    params_group.add_option(
+    params_group.add_argument(
         "--window", type=int, default=40, help="Synteny window size"
     )
-    params_group.add_option(
+    params_group.add_argument(
         "--cutoff",
         type=float,
         default=0.1,
         help="Minimum number of anchors to call synteny",
     )
     supported_scoring = ("collinear", "density")
-    params_group.add_option(
+    params_group.add_argument(
         "--scoring",
         choices=supported_scoring,
         default="collinear",
diff --git a/jcvi/compara/synteny.py b/jcvi/compara/synteny.py
index 9b048356..9e891ec0 100755
--- a/jcvi/compara/synteny.py
+++ b/jcvi/compara/synteny.py
@@ -410,13 +410,13 @@ def check_beds(hintfile, p, opts, sorted=True):
     return qbed, sbed, qorder, sorder, is_self
 
 
-def add_options(p, args, dist=10):
+def add_arguments(p, args, dist=10):
     """
     scan and liftover has similar interfaces, so share common options
     returns opts, files
     """
     p.set_beds()
-    p.add_option(
+    p.add_argument(
         "--dist", default=dist, type=int, help="Extent of flanking regions to search"
     )
 
@@ -569,7 +569,7 @@ def assemble(args):
     from jcvi.formats.fasta import some
 
     p = OptionParser(assemble.__doc__)
-    p.add_option(
+    p.add_argument(
         "--no_strip_names",
         default=False,
         action="store_true",
@@ -784,7 +784,7 @@ def toaligns(args):
     with the Block ID.
     """
     p = OptionParser(toaligns.__doc__)
-    p.add_option("--prefix", default="b", help="Prefix to the block id")
+    p.add_argument("--prefix", default="b", help="Prefix to the block id")
     p.set_outfile()
     opts, args = p.parse_args(args)
 
@@ -813,8 +813,8 @@ def mcscanq(args):
     graphics.karyotype and graphics.synteny.
     """
     p = OptionParser(mcscanq.__doc__)
-    p.add_option("--color", help="Add color highlight, used in plotting")
-    p.add_option(
+    p.add_argument("--color", help="Add color highlight, used in plotting")
+    p.add_argument(
         "--invert", default=False, action="store_true", help="Invert query and subject"
     )
     opts, args = p.parse_args(args)
@@ -842,7 +842,7 @@ def spa(args):
     from jcvi.utils.cbook import uniqify
 
     p = OptionParser(spa.__doc__)
-    p.add_option(
+    p.add_argument(
         "--unmapped",
         default=False,
         action="store_true",
@@ -899,10 +899,10 @@ def rebuild(args):
     Rebuild anchors file from pre-built blocks file.
     """
     p = OptionParser(rebuild.__doc__)
-    p.add_option(
+    p.add_argument(
         "--header", default=False, action="store_true", help="First line is header"
     )
-    p.add_option(
+    p.add_argument(
         "--write_blast",
         default=False,
         action="store_true",
@@ -990,7 +990,7 @@ def matrix(args):
     """
 
     p = OptionParser(matrix.__doc__)
-    p.add_option("--seqids", help="File with seqids")
+    p.add_argument("--seqids", help="File with seqids")
     opts, args = p.parse_args(args)
 
     if len(args) != 3:
@@ -1056,22 +1056,22 @@ def simple(args):
     block_id  seqidB    startB    endB     bpSpanB  GeneB1   GeneB2  geneSpanB
     """
     p = OptionParser(simple.__doc__)
-    p.add_option(
+    p.add_argument(
         "--rich", default=False, action="store_true", help="Output additional columns"
     )
-    p.add_option(
+    p.add_argument(
         "--coords",
         default=False,
         action="store_true",
         help="Output columns with base coordinates",
     )
-    p.add_option(
+    p.add_argument(
         "--bed",
         default=False,
         action="store_true",
         help="Generate BED file for the blocks",
     )
-    p.add_option(
+    p.add_argument(
         "--noheader", default=False, action="store_true", help="Don't output header"
     )
     p.set_beds()
@@ -1240,18 +1240,18 @@ def screen(args):
 
     p = OptionParser(screen.__doc__)
     p.set_beds()
-    p.add_option("--ids", help="File with block IDs (0-based)")
-    p.add_option("--seqids", help="File with seqids")
-    p.add_option("--seqpairs", help="File with seqpairs")
-    p.add_option(
+    p.add_argument("--ids", help="File with block IDs (0-based)")
+    p.add_argument("--seqids", help="File with seqids")
+    p.add_argument("--seqpairs", help="File with seqpairs")
+    p.add_argument(
         "--intrabound",
         default=300,
         type=int,
         help="Lower bound of intra-chromosomal blocks (only for self comparison)",
     )
-    p.add_option("--minspan", default=0, type=int, help="Only blocks with span >=")
-    p.add_option("--minsize", default=0, type=int, help="Only blocks with anchors >=")
-    p.add_option(
+    p.add_argument("--minspan", default=0, type=int, help="Only blocks with span >=")
+    p.add_argument("--minsize", default=0, type=int, help="Only blocks with anchors >=")
+    p.add_argument(
         "--simple", action="store_true", help="Write simple anchorfile with block ends"
     )
     opts, args = p.parse_args(args)
@@ -1358,7 +1358,7 @@ def summary(args):
     from jcvi.utils.cbook import SummaryStats
 
     p = OptionParser(summary.__doc__)
-    p.add_option("--prefix", help="Generate per block stats")
+    p.add_argument("--prefix", help="Generate per block stats")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -1454,20 +1454,22 @@ def mcscan(args):
     tandem cluster as one line, tab separated.
     """
     p = OptionParser(mcscan.__doc__)
-    p.add_option("--iter", default=100, type=int, help="Max number of chains to output")
-    p.add_option(
+    p.add_argument(
+        "--iter", default=100, type=int, help="Max number of chains to output"
+    )
+    p.add_argument(
         "--ascii",
         default=False,
         action="store_true",
         help="Output symbols rather than gene names",
     )
-    p.add_option(
+    p.add_argument(
         "--Nm", default=10, type=int, help="Clip block ends to allow slight overlaps"
     )
-    p.add_option(
+    p.add_argument(
         "--trackids", action="store_true", help="Track block IDs in separate file"
     )
-    p.add_option(
+    p.add_argument(
         "--mergetandem",
         default=None,
         help="merge tandems genes in output acoording to PATH-TO-TANDEM_FILE, "
@@ -1579,13 +1581,13 @@ def depth(args):
     from jcvi.graphics.base import latex
 
     p = OptionParser(depth.__doc__)
-    p.add_option("--depthfile", help="Generate file with gene and depth")
-    p.add_option(
+    p.add_argument("--depthfile", help="Generate file with gene and depth")
+    p.add_argument(
         "--histogram", default=False, action="store_true", help="Plot histograms in PDF"
     )
-    p.add_option("--xmax", type=int, help="x-axis maximum to display in plot")
-    p.add_option("--title", default=None, help="Title to display in plot")
-    p.add_option("--quota", help="Force to use this quota, e.g. 1:1, 1:2 ...")
+    p.add_argument("--xmax", type=int, help="x-axis maximum to display in plot")
+    p.add_argument("--title", default=None, help="Title to display in plot")
+    p.add_argument("--quota", help="Force to use this quota, e.g. 1:1, 1:2 ...")
     p.set_beds()
 
     opts, args = p.parse_args(args)
@@ -1721,13 +1723,13 @@ def breakpoint(args):
     from jcvi.utils.range import range_interleave
 
     p = OptionParser(breakpoint.__doc__)
-    p.add_option(
+    p.add_argument(
         "--xdist", type=int, default=20, help="xdist (in related genome) cutoff"
     )
-    p.add_option(
+    p.add_argument(
         "--ydist", type=int, default=200000, help="ydist (in current genome) cutoff"
     )
-    p.add_option("-n", type=int, default=5, help="number of markers in a block")
+    p.add_argument("-n", type=int, default=5, help="number of markers in a block")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -1758,7 +1760,7 @@ def scan(args):
     pull out syntenic anchors from blastfile based on single-linkage algorithm
     """
     p = OptionParser(scan.__doc__)
-    p.add_option(
+    p.add_argument(
         "-n",
         "--min_size",
         dest="n",
@@ -1766,21 +1768,21 @@ def scan(args):
         default=4,
         help="minimum number of anchors in a cluster",
     )
-    p.add_option(
+    p.add_argument(
         "--intrabound",
         default=300,
         type=int,
         help="Lower bound of intra-chromosomal blocks (only for self comparison)",
     )
-    p.add_option("--liftover", help="Scan BLAST file to find extra anchors")
-    p.add_option(
+    p.add_argument("--liftover", help="Scan BLAST file to find extra anchors")
+    p.add_argument(
         "--liftover_dist",
         type=int,
         help="Distance to extend from liftover. Defaults to half of --dist",
     )
     p.set_stripnames()
 
-    blast_file, anchor_file, dist, opts = add_options(p, args, dist=20)
+    blast_file, anchor_file, dist, opts = add_arguments(p, args, dist=20)
     qbed, sbed, qorder, sorder, is_self = check_beds(blast_file, p, opts)
 
     intrabound = opts.intrabound
@@ -1836,7 +1838,7 @@ def liftover(args):
     p = OptionParser(liftover.__doc__)
     p.set_stripnames()
 
-    blast_file, anchor_file, dist, opts = add_options(p, args)
+    blast_file, anchor_file, dist, opts = add_arguments(p, args)
     qbed, sbed, qorder, sorder, is_self = check_beds(blast_file, p, opts)
 
     filtered_blast = read_blast(
diff --git a/jcvi/formats/agp.py b/jcvi/formats/agp.py
index c91d6b14..76e40122 100644
--- a/jcvi/formats/agp.py
+++ b/jcvi/formats/agp.py
@@ -918,7 +918,7 @@ def fromcsv(args):
     from jcvi.formats.sizes import Sizes
 
     p = OptionParser(fromcsv.__doc__)
-    p.add_option("--evidence", default="map", help="Linkage evidence to add in AGP")
+    p.add_argument("--evidence", default="map", help="Linkage evidence to add in AGP")
     opts, args = p.parse_args(args)
 
     if len(args) != 3:
@@ -1113,7 +1113,7 @@ def format(args):
     from jcvi.formats.base import DictFile
 
     p = OptionParser(format.__doc__)
-    p.add_option("--switchcomponent", help="Switch component id based on")
+    p.add_argument("--switchcomponent", help="Switch component id based on")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -1147,13 +1147,13 @@ def frombed(args):
     columns. With the 4-th column indicating the new object.
     """
     p = OptionParser(frombed.__doc__)
-    p.add_option(
+    p.add_argument(
         "--gapsize",
         default=100,
         type=int,
         help="Insert gaps of size",
     )
-    p.add_option("--evidence", default="map", help="Linkage evidence to add in AGP")
+    p.add_argument("--evidence", default="map", help="Linkage evidence to add in AGP")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -1259,7 +1259,7 @@ def stats(args):
     from jcvi.utils.table import tabulate
 
     p = OptionParser(stats.__doc__)
-    p.add_option(
+    p.add_argument(
         "--warn",
         default=False,
         action="store_true",
@@ -1311,7 +1311,7 @@ def cut(args):
     Cut at the boundaries of the ranges in the bedfile.
     """
     p = OptionParser(cut.__doc__)
-    p.add_option("--sep", default=".", help="Separator for splits")
+    p.add_argument("--sep", default=".", help="Separator for splits")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -1383,36 +1383,36 @@ def mask(args):
     (--splitsingle).
     """
     p = OptionParser(mask.__doc__)
-    p.add_option(
+    p.add_argument(
         "--splitobject",
         default=False,
         action="store_true",
         help="Create new names for object",
     )
-    p.add_option(
+    p.add_argument(
         "--splitcomponent",
         default=False,
         action="store_true",
         help="Create new names for component",
     )
-    p.add_option(
+    p.add_argument(
         "--splitsingle",
         default=False,
         action="store_true",
         help="Do not remove base on single point",
     )
-    p.add_option(
+    p.add_argument(
         "--gaptype",
         default="scaffold",
         help="Masked region has gap type of",
     )
-    p.add_option(
+    p.add_argument(
         "--noretain",
         default=False,
         action="store_true",
         help="Do not retain old names for non-split objects",
     )
-    p.add_option("--sep", default=".", help="Separator for splits")
+    p.add_argument("--sep", default=".", help="Separator for splits")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -1532,13 +1532,13 @@ def reindex(args):
     the target coordinates.
     """
     p = OptionParser(reindex.__doc__)
-    p.add_option(
+    p.add_argument(
         "--nogaps",
         default=False,
         action="store_true",
         help="Remove all gap lines",
     )
-    p.add_option(
+    p.add_argument(
         "--inplace",
         default=False,
         action="store_true",
@@ -1695,13 +1695,13 @@ def tpf(args):
     Can optionally output scaffold gaps.
     """
     p = OptionParser(tpf.__doc__)
-    p.add_option(
+    p.add_argument(
         "--noversion",
         default=False,
         action="store_true",
         help="Remove trailing accession versions",
     )
-    p.add_option(
+    p.add_argument(
         "--gaps",
         default=False,
         action="store_true",
@@ -1739,25 +1739,25 @@ def bed(args):
     from jcvi.formats.obo import validate_term
 
     p = OptionParser(bed.__doc__)
-    p.add_option(
+    p.add_argument(
         "--gaps",
         default=False,
         action="store_true",
         help="Only print bed lines for gaps",
     )
-    p.add_option(
+    p.add_argument(
         "--nogaps",
         default=False,
         action="store_true",
         help="Do not print bed lines for gaps",
     )
-    p.add_option(
+    p.add_argument(
         "--bed12",
         default=False,
         action="store_true",
         help="Produce bed12 formatted output",
     )
-    p.add_option(
+    p.add_argument(
         "--component",
         default=False,
         action="store_true",
@@ -1768,14 +1768,14 @@ def bed(args):
         "GFF specific parameters",
         "Note: If not specified, output will be in `bed` format",
     )
-    g1.add_option(
+    g1.add_argument(
         "--gff",
         default=False,
         action="store_true",
         help="Produce gff3 formatted output. By default, ignores AGP gap lines",
     )
-    g1.add_option("--source", default="MGSC", help="Specify a gff3 source")
-    g1.add_option(
+    g1.add_argument("--source", default="MGSC", help="Specify a gff3 source")
+    g1.add_argument(
         "--feature",
         default="golden_path_fragment",
         help="Specify a gff3 feature type",
@@ -1849,19 +1849,19 @@ def extendbed(args):
     from jcvi.formats.sizes import Sizes
 
     p = OptionParser(extendbed.__doc__)
-    p.add_option(
+    p.add_argument(
         "--nogaps",
         default=False,
         action="store_true",
         help="Do not print bed lines for gaps",
     )
-    p.add_option(
+    p.add_argument(
         "--bed12",
         default=False,
         action="store_true",
         help="Produce bed12 formatted output",
     )
-    p.add_option(
+    p.add_argument(
         "--gff",
         default=False,
         action="store_true",
@@ -1936,14 +1936,14 @@ def gaps(args):
     from jcvi.graphics.histogram import loghistogram
 
     p = OptionParser(gaps.__doc__)
-    p.add_option(
+    p.add_argument(
         "--merge",
         dest="merge",
         default=False,
         action="store_true",
         help="Merge adjacent gaps (to conform to AGP specification)",
     )
-    p.add_option(
+    p.add_argument(
         "--header",
         default=False,
         action="store_true",
@@ -2033,7 +2033,7 @@ def tidy(args):
     Final output is in `.tidy.agp`.
     """
     p = OptionParser(tidy.__doc__)
-    p.add_option(
+    p.add_argument(
         "--nogaps",
         default=False,
         action="store_true",
@@ -2098,14 +2098,14 @@ def build(args):
     Build targetfasta based on info from agpfile
     """
     p = OptionParser(build.__doc__)
-    p.add_option(
+    p.add_argument(
         "--newagp",
         dest="newagp",
         default=False,
         action="store_true",
         help="Check components to trim dangling N's",
     )
-    p.add_option(
+    p.add_argument(
         "--novalidate",
         dest="novalidate",
         default=False,
diff --git a/jcvi/formats/base.py b/jcvi/formats/base.py
index 0d8b6b12..4de649f3 100644
--- a/jcvi/formats/base.py
+++ b/jcvi/formats/base.py
@@ -570,7 +570,7 @@ def seqids(args):
     A03,A02,A01
     """
     p = OptionParser(seqids.__doc__)
-    p.add_option("--pad0", default=0, help="How many zeros to pad")
+    p.add_argument("--pad0", default=0, help="How many zeros to pad")
     opts, args = p.parse_args(args)
 
     if len(args) != 3:
@@ -702,7 +702,7 @@ def flatten(args):
 
     p = OptionParser(flatten.__doc__)
     p.set_sep(sep=",")
-    p.add_option(
+    p.add_argument(
         "--zipflatten",
         default=None,
         dest="zipsep",
@@ -741,7 +741,7 @@ def unflatten(args):
     Given a list of ids, one per line, unflatten the list onto a single line with sep.
     """
     p = OptionParser(unflatten.__doc__)
-    p.add_option("--sep", default=",", help="Separator when joining ids")
+    p.add_argument("--sep", default=",", help="Separator when joining ids")
     p.set_outfile()
     opts, args = p.parse_args(args)
 
@@ -785,11 +785,13 @@ def group(args):
 
     p = OptionParser(group.__doc__)
     p.set_sep()
-    p.add_option("--groupby", default=None, type=int, help="Default column to groupby")
-    p.add_option(
+    p.add_argument(
+        "--groupby", default=None, type=int, help="Default column to groupby"
+    )
+    p.add_argument(
         "--groupsep", default=",", help="Separator to join the grouped elements"
     )
-    p.add_option(
+    p.add_argument(
         "--nouniq",
         default=False,
         action="store_true",
@@ -896,14 +898,16 @@ def split(args):
     """
     p = OptionParser(split.__doc__)
     mode_choices = ("batch", "cycle", "optimal")
-    p.add_option("--all", default=False, action="store_true", help="split all records")
-    p.add_option(
+    p.add_argument(
+        "--all", default=False, action="store_true", help="split all records"
+    )
+    p.add_argument(
         "--mode",
         default="optimal",
         choices=mode_choices,
         help="Mode when splitting records",
     )
-    p.add_option(
+    p.add_argument(
         "--format", choices=("fasta", "fastq", "txt", "clust"), help="input file format"
     )
 
@@ -941,21 +945,21 @@ def join(args):
       in each file.
     """
     p = OptionParser(join.__doc__)
-    p.add_option(
+    p.add_argument(
         "--column", default="0", help="0-based column id, multiple values allowed"
     )
     p.set_sep(multiple=True)
-    p.add_option(
+    p.add_argument(
         "--noheader", default=False, action="store_true", help="Do not print header"
     )
-    p.add_option("--na", default="na", help="Value for unjoined data")
-    p.add_option(
+    p.add_argument("--na", default="na", help="Value for unjoined data")
+    p.add_argument(
         "--compact",
         default=False,
         action="store_true",
         help="Do not repeat pivotal columns in output",
     )
-    p.add_option(
+    p.add_argument(
         "--keysep",
         default=",",
         help="specify separator joining multiple elements in the key column"
@@ -1046,11 +1050,11 @@ def subset(args):
     """
 
     p = OptionParser(subset.__doc__)
-    p.add_option(
+    p.add_argument(
         "--column", default="0", help="0-based column id, multiple values allowed"
     )
     p.set_sep(multiple=True)
-    p.add_option(
+    p.add_argument(
         "--pivot",
         default=1,
         type=int,
@@ -1127,7 +1131,7 @@ def setop(args):
     from natsort import natsorted
 
     p = OptionParser(setop.__doc__)
-    p.add_option(
+    p.add_argument(
         "--column",
         default=0,
         type=int,
diff --git a/jcvi/formats/bed.py b/jcvi/formats/bed.py
index 33872f4b..4194b043 100755
--- a/jcvi/formats/bed.py
+++ b/jcvi/formats/bed.py
@@ -503,7 +503,7 @@ def gaps(args):
     from pybedtools import BedTool
 
     p = OptionParser(gaps.__doc__)
-    p.add_option(
+    p.add_argument(
         "--na_in",
         help="Add '_na_in_xxx' to gap name, use comma to separate, "
         + "e.g. --na_in=chr1,chr2 to note if gap is missing in chr1 or "
@@ -511,7 +511,7 @@ def gaps(args):
         + "missing seqids happens to be the seqid of the current feature, "
         + "it will not be reported.",
     )
-    p.add_option("--minsize", default=1000, type=int, help="Minimum gap size")
+    p.add_argument("--minsize", default=1000, type=int, help="Minimum gap size")
     p.set_outfile()
     opts, args = p.parse_args(args)
 
@@ -560,7 +560,7 @@ def closest(args):
     from pybedtools import BedTool
 
     p = OptionParser(closest.__doc__)
-    p.add_option("--maxdist", default=5000, help="Maximum distance")
+    p.add_argument("--maxdist", default=5000, help="Maximum distance")
     p.set_outfile()
     opts, args = p.parse_args(args)
 
@@ -593,8 +593,8 @@ def format(args):
     Re-format BED file, e.g. switch sequence ids.
     """
     p = OptionParser(format.__doc__)
-    p.add_option("--prefix", help="Add prefix to name column (4th)")
-    p.add_option("--switch", help="Switch seqids based on two-column file")
+    p.add_argument("--prefix", help="Add prefix to name column (4th)")
+    p.add_argument("--switch", help="Switch seqids based on two-column file")
     p.set_outfile()
     opts, args = p.parse_args(args)
 
@@ -660,7 +660,7 @@ def tiling(args):
     stackoverflow source.
     """
     p = OptionParser(tiling.__doc__)
-    p.add_option(
+    p.add_argument(
         "--overlap",
         default=3000,
         type=int,
@@ -739,7 +739,7 @@ def chain(args):
     Chain BED segments together.
     """
     p = OptionParser(chain.__doc__)
-    p.add_option("--dist", default=100000, help="Chaining distance")
+    p.add_argument("--dist", default=100000, help="Chaining distance")
     p.set_outfile()
     opts, args = p.parse_args(args)
 
@@ -884,9 +884,9 @@ def seqids(args):
     Print out all seqids on one line. Useful for graphics.karyotype.
     """
     p = OptionParser(seqids.__doc__)
-    p.add_option("--maxn", default=100, type=int, help="Maximum number of seqids")
-    p.add_option("--prefix", help="Seqids must start with")
-    p.add_option("--exclude", default="random", help="Seqids should not contain")
+    p.add_argument("--maxn", default=100, type=int, help="Maximum number of seqids")
+    p.add_argument("--prefix", help="Seqids must start with")
+    p.add_argument("--exclude", default="random", help="Seqids should not contain")
     opts, args = p.parse_args(args)
 
     if len(args) < 1:
@@ -994,16 +994,16 @@ def filter(args):
     Filter the bedfile to retain records between certain size range.
     """
     p = OptionParser(filter.__doc__)
-    p.add_option("--minsize", default=0, type=int, help="Minimum feature length")
-    p.add_option(
+    p.add_argument("--minsize", default=0, type=int, help="Minimum feature length")
+    p.add_argument(
         "--maxsize", default=1000000000, type=int, help="Minimum feature length"
     )
-    p.add_option(
+    p.add_argument(
         "--minaccn",
         type=int,
         help="Minimum value of accn, useful to filter based on coverage",
     )
-    p.add_option("--minscore", type=int, help="Minimum score")
+    p.add_argument("--minscore", type=int, help="Minimum score")
     p.set_outfile()
 
     opts, args = p.parse_args(args)
@@ -1060,7 +1060,7 @@ def mergebydepth(args):
     Similar to mergeBed, but only returns regions beyond certain depth.
     """
     p = OptionParser(mergebydepth.__doc__)
-    p.add_option("--mindepth", default=3, type=int, help="Minimum depth required")
+    p.add_argument("--mindepth", default=3, type=int, help="Minimum depth required")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -1131,9 +1131,9 @@ def longest(args):
     from jcvi.formats.sizes import Sizes
 
     p = OptionParser(longest.__doc__)
-    p.add_option("--maxsize", default=20000, type=int, help="Limit max size")
-    p.add_option("--minsize", default=60, type=int, help="Limit min size")
-    p.add_option(
+    p.add_argument("--maxsize", default=20000, type=int, help="Limit max size")
+    p.add_argument("--minsize", default=60, type=int, help="Limit min size")
+    p.add_argument(
         "--precedence", default="Medtr", help="Accessions with prefix take precedence"
     )
     opts, args = p.parse_args(args)
@@ -1216,7 +1216,7 @@ def fix(args):
     Fix non-standard bed files. One typical problem is start > end.
     """
     p = OptionParser(fix.__doc__)
-    p.add_option("--minspan", default=0, type=int, help="Enforce minimum span")
+    p.add_argument("--minspan", default=0, type=int, help="Enforce minimum span")
     p.set_outfile()
     opts, args = p.parse_args(args)
 
@@ -1267,7 +1267,7 @@ def some(args):
     from jcvi.utils.cbook import gene_name
 
     p = OptionParser(some.__doc__)
-    p.add_option(
+    p.add_argument(
         "-v",
         dest="inverse",
         default=False,
@@ -1314,8 +1314,10 @@ def uniq(args):
     from jcvi.formats.sizes import Sizes
 
     p = OptionParser(uniq.__doc__)
-    p.add_option("--sizes", help="Use sequence length as score")
-    p.add_option("--mode", default="span", choices=("span", "score"), help="Pile mode")
+    p.add_argument("--sizes", help="Use sequence length as score")
+    p.add_argument(
+        "--mode", default="span", choices=("span", "score"), help="Pile mode"
+    )
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -1404,15 +1406,15 @@ def bins(args):
     """
 
     p = OptionParser(bins.__doc__)
-    p.add_option("--binsize", default=100000, type=int, help="Size of the bins")
-    p.add_option("--subtract", help="Subtract bases from window")
-    p.add_option(
+    p.add_argument("--binsize", default=100000, type=int, help="Size of the bins")
+    p.add_argument("--subtract", help="Subtract bases from window")
+    p.add_argument(
         "--mode",
         default="span",
         choices=("span", "count", "score"),
         help="Accumulate feature based on",
     )
-    p.add_option(
+    p.add_argument(
         "--nomerge", default=False, action="store_true", help="Do not merge features"
     )
     opts, args = p.parse_args(args)
@@ -1506,7 +1508,7 @@ def pile(args):
     from jcvi.utils.grouper import Grouper
 
     p = OptionParser(pile.__doc__)
-    p.add_option("--minOverlap", default=0, type=int, help="Minimum overlap required")
+    p.add_argument("--minOverlap", default=0, type=int, help="Minimum overlap required")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -1535,8 +1537,8 @@ def index(args):
     so that a bedgraph file can be generated and indexed.
     """
     p = OptionParser(index.__doc__)
-    p.add_option("--fasta", help="Generate bedgraph and index")
-    p.add_option("--query", help="Chromosome location")
+    p.add_argument("--fasta", help="Generate bedgraph and index")
+    p.add_argument("--query", help="Chromosome location")
     p.set_outfile()
 
     opts, args = p.parse_args(args)
@@ -1695,7 +1697,7 @@ def evaluate(args):
     from jcvi.formats.sizes import Sizes
 
     p = OptionParser(evaluate.__doc__)
-    p.add_option("--query", help="Chromosome location")
+    p.add_argument("--query", help="Chromosome location")
     opts, args = p.parse_args(args)
 
     if len(args) != 3:
@@ -1811,7 +1813,7 @@ def distance(args):
     distances, which can be used to plot histogram, etc.
     """
     p = OptionParser(distance.__doc__)
-    p.add_option(
+    p.add_argument(
         "--distmode",
         default="ss",
         choices=("ss", "ee"),
@@ -1860,14 +1862,14 @@ def sample(args):
     from jcvi.assembly.coverage import Coverage
 
     p = OptionParser(sample.__doc__)
-    p.add_option(
+    p.add_argument(
         "--raindrop",
         default=0,
         type=int,
         help="Raindrop selection, ignores all other options",
     )
-    p.add_option("--max", default=10, type=int, help="Max depth allowed")
-    p.add_option(
+    p.add_argument("--max", default=10, type=int, help="Max depth allowed")
+    p.add_argument(
         "--targetsize", type=int, help="Sample bed file to get target base number"
     )
     p.set_outfile()
@@ -1950,13 +1952,13 @@ def bedpe(args):
     from jcvi.assembly.coverage import bed_to_bedpe
 
     p = OptionParser(bedpe.__doc__)
-    p.add_option(
+    p.add_argument(
         "--span", default=False, action="store_true", help="Write span bed file"
     )
-    p.add_option(
+    p.add_argument(
         "--strand", default=False, action="store_true", help="Write the strand columns"
     )
-    p.add_option("--mates", help="Check the library stats from .mates file")
+    p.add_argument("--mates", help="Check the library stats from .mates file")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -2215,10 +2217,10 @@ def summary(args):
     Sum the total lengths of the intervals.
     """
     p = OptionParser(summary.__doc__)
-    p.add_option(
+    p.add_argument(
         "--sizes", default=False, action="store_true", help="Write .sizes file"
     )
-    p.add_option(
+    p.add_argument(
         "--all",
         default=False,
         action="store_true",
@@ -2258,7 +2260,7 @@ def sort(args):
     `sort` command.
     """
     p = OptionParser(sort.__doc__)
-    p.add_option(
+    p.add_argument(
         "-i",
         "--inplace",
         dest="inplace",
@@ -2266,20 +2268,20 @@ def sort(args):
         action="store_true",
         help="Sort bed file in place",
     )
-    p.add_option(
+    p.add_argument(
         "-u",
         dest="unique",
         default=False,
         action="store_true",
         help="Uniqify the bed file",
     )
-    p.add_option(
+    p.add_argument(
         "--accn",
         default=False,
         action="store_true",
         help="Sort based on the accessions",
     )
-    p.add_option(
+    p.add_argument(
         "--num",
         default=False,
         action="store_true",
@@ -2333,19 +2335,19 @@ def mates(args):
     Generate the mates file by inferring from the names.
     """
     p = OptionParser(mates.__doc__)
-    p.add_option(
+    p.add_argument(
         "--lib",
         default=False,
         action="store_true",
         help="Output library information along with pairs",
     )
-    p.add_option(
+    p.add_argument(
         "--nointra",
         default=False,
         action="store_true",
         help="Remove mates that are intra-scaffold",
     )
-    p.add_option(
+    p.add_argument(
         "--prefix",
         default=False,
         action="store_true",
@@ -2431,23 +2433,25 @@ def flanking(args):
     from numpy import array, argsort
 
     p = OptionParser(flanking.__doc__)
-    p.add_option(
+    p.add_argument(
         "--chrom",
         default=None,
         type=str,
         help="chrom name of the position in query. Make sure it matches bedfile.",
     )
-    p.add_option(
+    p.add_argument(
         "--coord", default=None, type=int, help="coordinate of the position in query."
     )
-    p.add_option("-n", default=10, type=int, help="number of flanking features to get")
-    p.add_option(
+    p.add_argument(
+        "-n", default=10, type=int, help="number of flanking features to get"
+    )
+    p.add_argument(
         "--side",
         default="both",
         choices=("upstream", "downstream", "both"),
         help="which side to get flanking features",
     )
-    p.add_option(
+    p.add_argument(
         "--max_d", default=None, type=int, help="features <= max_d away from position"
     )
     p.set_outfile()
diff --git a/jcvi/formats/blast.py b/jcvi/formats/blast.py
index d80dff35..72a43314 100644
--- a/jcvi/formats/blast.py
+++ b/jcvi/formats/blast.py
@@ -296,13 +296,13 @@ def filter(args):
     - noself: remove self-self hits
     """
     p = OptionParser(filter.__doc__)
-    p.add_option("--score", dest="score", default=0, type=int, help="Score cutoff")
+    p.add_argument("--score", dest="score", default=0, type=int, help="Score cutoff")
     p.set_align(pctid=95, hitlen=100, evalue=0.01)
-    p.add_option(
+    p.add_argument(
         "--noself", default=False, action="store_true", help="Remove self-self hits"
     )
-    p.add_option("--ids", help="Path to file with ids to retain")
-    p.add_option(
+    p.add_argument("--ids", help="Path to file with ids to retain")
+    p.add_argument(
         "--inverse",
         default=False,
         action="store_true",
@@ -527,8 +527,8 @@ def annotation(args):
     from jcvi.formats.base import DictFile
 
     p = OptionParser(annotation.__doc__)
-    p.add_option("--queryids", help="Query IDS file to switch")
-    p.add_option("--subjectids", help="Subject IDS file to switch")
+    p.add_argument("--queryids", help="Query IDS file to switch")
+    p.add_argument("--subjectids", help="Subject IDS file to switch")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -562,7 +562,7 @@ def completeness(args):
     from jcvi.utils.cbook import SummaryStats
 
     p = OptionParser(completeness.__doc__)
-    p.add_option("--ids", help="Save ids that are over 50% complete")
+    p.add_argument("--ids", help="Save ids that are over 50% complete")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -627,7 +627,7 @@ def annotate(args):
 
     p = OptionParser(annotate.__doc__)
     p.set_align(pctid=94, hitlen=500)
-    p.add_option("--hang", default=500, type=int, help="Maximum overhang length")
+    p.add_argument("--hang", default=500, type=int, help="Maximum overhang length")
     opts, args = p.parse_args(args)
 
     if len(args) != 3:
@@ -665,13 +665,13 @@ def top10(args):
     from jcvi.formats.base import DictFile
 
     p = OptionParser(top10.__doc__)
-    p.add_option(
+    p.add_argument(
         "--top",
         default=10,
         type=int,
         help="Top N taxa to extract",
     )
-    p.add_option(
+    p.add_argument(
         "--ids",
         default=None,
         help="Two column ids file to query seqid",
@@ -701,25 +701,25 @@ def sort(args):
     sort is 'in-place'.
     """
     p = OptionParser(sort.__doc__)
-    p.add_option(
+    p.add_argument(
         "--query",
         default=False,
         action="store_true",
         help="Sort by query position",
     )
-    p.add_option(
+    p.add_argument(
         "--ref",
         default=False,
         action="store_true",
         help="Sort by reference position",
     )
-    p.add_option(
+    p.add_argument(
         "--refscore",
         default=False,
         action="store_true",
         help="Sort by reference name, then score descending",
     )
-    p.add_option(
+    p.add_argument(
         "--coords",
         default=False,
         action="store_true",
@@ -774,19 +774,19 @@ def cscore(args):
     from jcvi.utils.cbook import gene_name
 
     p = OptionParser(cscore.__doc__)
-    p.add_option(
+    p.add_argument(
         "--cutoff",
         default=0.9999,
         type=float,
         help="Minimum C-score to report",
     )
-    p.add_option(
+    p.add_argument(
         "--pct",
         default=False,
         action="store_true",
         help="Also include pct as last column",
     )
-    p.add_option(
+    p.add_argument(
         "--writeblast",
         default=False,
         action="store_true",
@@ -939,7 +939,7 @@ def chain(args):
     Chain adjacent HSPs together to form larger HSP.
     """
     p = OptionParser(chain.__doc__)
-    p.add_option(
+    p.add_argument(
         "--dist",
         dest="dist",
         default=100,
@@ -1042,29 +1042,29 @@ def covfilter(args):
 
     p = OptionParser(covfilter.__doc__)
     p.set_align(pctid=95, pctcov=50)
-    p.add_option(
+    p.add_argument(
         "--scov",
         default=False,
         action="store_true",
         help="Subject coverage instead of query",
     )
-    p.add_option(
+    p.add_argument(
         "--supermap", action="store_true", help="Use supermap instead of union"
     )
-    p.add_option(
+    p.add_argument(
         "--ids",
         dest="ids",
         default=None,
         help="Print out the ids that satisfy",
     )
-    p.add_option(
+    p.add_argument(
         "--list",
         dest="list",
         default=False,
         action="store_true",
         help="List the id% and cov% per gene",
     )
-    p.add_option(
+    p.add_argument(
         "--iterby",
         dest="iterby",
         default="query",
@@ -1264,19 +1264,19 @@ def bed(args):
     from .bed import sort as bed_sort, mergeBed
 
     p = OptionParser(bed.__doc__)
-    p.add_option(
+    p.add_argument(
         "--swap",
         default=False,
         action="store_true",
         help="Write query positions",
     )
-    p.add_option(
+    p.add_argument(
         "--both",
         default=False,
         action="store_true",
         help="Generate one line for each of query and subject",
     )
-    p.add_option(
+    p.add_argument(
         "--merge",
         default=None,
         type=int,
@@ -1345,7 +1345,7 @@ def anchors(args):
     """
     p = OptionParser(anchors.__doc__)
     p.set_outfile()
-    p.add_option(
+    p.add_argument(
         "--best", default=False, action="store_true", help="Keep only the best hit"
     )
     opts, args = p.parse_args(args)
@@ -1379,20 +1379,20 @@ def best(args):
     """
     p = OptionParser(best.__doc__)
 
-    p.add_option("-n", default=1, type=int, help="get best N hits")
-    p.add_option(
+    p.add_argument("-n", default=1, type=int, help="get best N hits")
+    p.add_argument(
         "--nosort",
         default=False,
         action="store_true",
         help="assume BLAST is already sorted",
     )
-    p.add_option(
+    p.add_argument(
         "--hsps",
         default=False,
         action="store_true",
         help="get all HSPs for the best pair",
     )
-    p.add_option(
+    p.add_argument(
         "--subject",
         default=False,
         action="store_true",
@@ -1445,13 +1445,13 @@ def summary(args):
     qryspan, pct_qryspan, refspan, pct_refspan
     """
     p = OptionParser(summary.__doc__)
-    p.add_option(
+    p.add_argument(
         "--strict",
         default=False,
         action="store_true",
         help="Strict 'gapless' mode. Exclude gaps from covered base.",
     )
-    p.add_option(
+    p.add_argument(
         "--tabular",
         default=False,
         action="store_true",
@@ -1483,17 +1483,17 @@ def subset(args):
     Otherwise the script will do nothing.
     """
     p = OptionParser(subset.__doc__)
-    p.add_option(
+    p.add_argument(
         "--qchrs",
         default=None,
         help="query chrs to extract, comma sep",
     )
-    p.add_option(
+    p.add_argument(
         "--schrs",
         default=None,
         help="subject chrs to extract, comma sep",
     )
-    p.add_option(
+    p.add_argument(
         "--convert",
         default=False,
         action="store_true",
diff --git a/jcvi/formats/chain.py b/jcvi/formats/chain.py
index 42986a69..e22dd764 100644
--- a/jcvi/formats/chain.py
+++ b/jcvi/formats/chain.py
@@ -136,7 +136,7 @@ def fromagp(args):
     from jcvi.formats.sizes import Sizes
 
     p = OptionParser(fromagp.__doc__)
-    p.add_option(
+    p.add_argument(
         "--novalidate", default=False, action="store_true", help="Do not validate AGP"
     )
     opts, args = p.parse_args(args)
@@ -219,13 +219,13 @@ def blat(args):
     Generate psl file using blat.
     """
     p = OptionParser(blat.__doc__)
-    p.add_option(
+    p.add_argument(
         "--minscore",
         default=100,
         type=int,
         help="Matches minus mismatches gap penalty",
     )
-    p.add_option(
+    p.add_argument(
         "--minid",
         default=98,
         type=int,
diff --git a/jcvi/formats/coords.py b/jcvi/formats/coords.py
index 904bc861..44a89d41 100644
--- a/jcvi/formats/coords.py
+++ b/jcvi/formats/coords.py
@@ -388,7 +388,7 @@ def coverage(args):
     jcvi.algorithms.supermap --filter query
     """
     p = OptionParser(coverage.__doc__)
-    p.add_option(
+    p.add_argument(
         "-c",
         dest="cutoff",
         default=0.5,
@@ -434,13 +434,13 @@ def annotate(args):
     overlaps: {0}.
     """
     p = OptionParser(annotate.__doc__.format(", ".join(Overlap_types)))
-    p.add_option(
+    p.add_argument(
         "--maxhang",
         default=100,
         type=int,
         help="Max hang to call dovetail overlap",
     )
-    p.add_option(
+    p.add_argument(
         "--all",
         default=False,
         action="store_true",
@@ -476,7 +476,7 @@ def summary(args):
     """
 
     p = OptionParser(summary.__doc__)
-    p.add_option(
+    p.add_argument(
         "-s",
         dest="single",
         default=False,
@@ -503,7 +503,7 @@ def filter(args):
     """
     p = OptionParser(filter.__doc__)
     p.set_align(pctid=0, hitlen=0)
-    p.add_option(
+    p.add_argument(
         "--overlap",
         default=False,
         action="store_true",
@@ -563,19 +563,19 @@ def bed(args):
     be beyond quality cutoff, say 50) in bed format
     """
     p = OptionParser(bed.__doc__)
-    p.add_option(
+    p.add_argument(
         "--query",
         default=False,
         action="store_true",
         help="print out query intervals rather than ref",
     )
-    p.add_option(
+    p.add_argument(
         "--pctid",
         default=False,
         action="store_true",
         help="use pctid in score",
     )
-    p.add_option(
+    p.add_argument(
         "--cutoff",
         dest="cutoff",
         default=0,
diff --git a/jcvi/formats/excel.py b/jcvi/formats/excel.py
index 21da5bcc..4e839cd3 100644
--- a/jcvi/formats/excel.py
+++ b/jcvi/formats/excel.py
@@ -165,13 +165,13 @@ def fromcsv(args):
     from jcvi.formats.base import flexible_cast
 
     p = OptionParser(fromcsv.__doc__)
-    p.add_option(
+    p.add_argument(
         "--noheader",
         default=False,
         action="store_true",
         help="Do not treat the first row as header",
     )
-    p.add_option("--rgb", default=-1, type=int, help="Show RGB color box")
+    p.add_argument("--rgb", default=-1, type=int, help="Show RGB color box")
     p.set_sep()
     opts, args = p.parse_args(args)
 
diff --git a/jcvi/formats/fasta.py b/jcvi/formats/fasta.py
index a70272cb..8671fcd7 100644
--- a/jcvi/formats/fasta.py
+++ b/jcvi/formats/fasta.py
@@ -443,7 +443,7 @@ def gc(args):
     Plot G+C content distribution.
     """
     p = OptionParser(gc.__doc__)
-    p.add_option("--binsize", default=500, type=int, help="Bin size to use")
+    p.add_argument("--binsize", default=500, type=int, help="Bin size to use")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -485,7 +485,7 @@ def trimsplit(args):
     from jcvi.utils.cbook import SummaryStats
 
     p = OptionParser(trimsplit.__doc__)
-    p.add_option(
+    p.add_argument(
         "--minlength", default=1000, type=int, help="Min length of contigs to keep"
     )
     opts, args = p.parse_args(args)
@@ -540,7 +540,9 @@ def qual(args):
     from jcvi.formats.sizes import Sizes
 
     p = OptionParser(qual.__doc__)
-    p.add_option("--qv", default=31, type=int, help="Dummy qv score for extended bases")
+    p.add_argument(
+        "--qv", default=31, type=int, help="Dummy qv score for extended bases"
+    )
     p.set_outfile()
     opts, args = p.parse_args(args)
 
@@ -567,7 +569,7 @@ def info(args):
     Run `sequence_info` on FASTA files. Generate a report per file.
     """
     p = OptionParser(info.__doc__)
-    p.add_option(
+    p.add_argument(
         "--gaps", default=False, action="store_true", help="Count number of gaps"
     )
     p.set_table()
@@ -594,10 +596,10 @@ def fromtab(args):
     """
     p = OptionParser(fromtab.__doc__)
     p.set_sep(sep=None)
-    p.add_option(
+    p.add_argument(
         "--noheader", default=False, action="store_true", help="Ignore first line"
     )
-    p.add_option("--replace", help="Replace spaces in name to char")
+    p.add_argument("--replace", help="Replace spaces in name to char")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -633,7 +635,7 @@ def longestorf(args):
     Find longest ORF for each sequence in fastafile.
     """
     p = OptionParser(longestorf.__doc__)
-    p.add_option("--ids", action="store_true", help="Generate table with ORF info")
+    p.add_argument("--ids", action="store_true", help="Generate table with ORF info")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -684,7 +686,7 @@ def ispcr(args):
     format: name, forward, reverse
     """
     p = OptionParser(ispcr.__doc__)
-    p.add_option(
+    p.add_argument(
         "-r",
         dest="rclip",
         default=1,
@@ -780,10 +782,10 @@ def clean(args):
     Remove irregular chars in FASTA seqs.
     """
     p = OptionParser(clean.__doc__)
-    p.add_option(
+    p.add_argument(
         "--fancy", default=False, action="store_true", help="Pretty print the sequence"
     )
-    p.add_option(
+    p.add_argument(
         "--canonical", default=False, action="store_true", help="Use only acgtnACGTN"
     )
     p.set_outfile()
@@ -822,31 +824,31 @@ def translate(args):
 
     transl_tables = [str(x) for x in range(1, 25)]
     p = OptionParser(translate.__doc__)
-    p.add_option(
+    p.add_argument(
         "--ids",
         default=False,
         action="store_true",
         help="Create .ids file with the complete/partial/gaps label",
     )
-    p.add_option(
+    p.add_argument(
         "--longest",
         default=False,
         action="store_true",
         help="Find the longest ORF from each input CDS",
     )
-    p.add_option(
+    p.add_argument(
         "--table",
         default=1,
         choices=transl_tables,
         help="Specify translation table to use",
     )
-    p.add_option(
+    p.add_argument(
         "--strip_names",
         default=False,
         action="store_true",
         help="Strip alternative splicing (e.g. At5g06540.1 -> At5g06540)",
     )
-    p.add_option(
+    p.add_argument(
         "--unique",
         default=False,
         action="store_true",
@@ -976,7 +978,7 @@ def filter(args):
     Filter the FASTA file to contain records with size >= or <= certain cutoff.
     """
     p = OptionParser(filter.__doc__)
-    p.add_option(
+    p.add_argument(
         "--less",
         default=False,
         action="store_true",
@@ -1023,8 +1025,8 @@ def pool(args):
     from jcvi.formats.base import longest_unique_prefix
 
     p = OptionParser(pool.__doc__)
-    p.add_option("--sep", default=".", help="Separator between prefix and name")
-    p.add_option(
+    p.add_argument("--sep", default=".", help="Separator between prefix and name")
+    p.add_argument(
         "--sequential", default=False, action="store_true", help="Add sequential IDs"
     )
     opts, args = p.parse_args(args)
@@ -1049,10 +1051,10 @@ def ids(args):
     Generate the FASTA headers without the '>'.
     """
     p = OptionParser(ids.__doc__)
-    p.add_option(
+    p.add_argument(
         "--until", default=None, help="Truncate the name and description at words"
     )
-    p.add_option(
+    p.add_argument(
         "--description",
         default=False,
         action="store_true",
@@ -1090,7 +1092,7 @@ def sort(args):
     Sort a list of sequences and output with sorted IDs, etc.
     """
     p = OptionParser(sort.__doc__)
-    p.add_option(
+    p.add_argument(
         "--sizes", default=False, action="store_true", help="Sort by decreasing size"
     )
 
@@ -1138,18 +1140,20 @@ def join(args):
     from jcvi.formats.sizes import Sizes
 
     p = OptionParser(join.__doc__)
-    p.add_option("--newid", default=None, help="New sequence ID")
-    p.add_option(
+    p.add_argument("--newid", default=None, help="New sequence ID")
+    p.add_argument(
         "--gapsize",
         default=100,
         type=int,
         help="Number of N's in between the sequences",
     )
-    p.add_option("--gaptype", default="contig", help="Gap type to use in the AGP file")
-    p.add_option(
+    p.add_argument(
+        "--gaptype", default="contig", help="Gap type to use in the AGP file"
+    )
+    p.add_argument(
         "--evidence", default="", help="Linkage evidence to report in the AGP file"
     )
-    p.add_option("--oo", help="Use .oo file generated by bambus")
+    p.add_argument("--oo", help="Use .oo file generated by bambus")
     opts, args = p.parse_args(args)
 
     nargs = len(args)
@@ -1218,10 +1222,10 @@ def summary(args):
     from natsort import natsort_key
 
     p = OptionParser(summary.__doc__)
-    p.add_option(
+    p.add_argument(
         "--suffix", default="Mb", help="make the base pair counts human readable"
     )
-    p.add_option("--ids", help="write the ids that have >= 50% N's")
+    p.add_argument("--ids", help="write the ids that have >= 50% N's")
     p.set_outfile()
 
     opts, args = p.parse_args(args)
@@ -1275,70 +1279,70 @@ def format(args):
     """
     sequential_choices = ("replace", "prefix", "suffix")
     p = OptionParser(format.__doc__)
-    p.add_option(
+    p.add_argument(
         "--pairs",
         default=False,
         action="store_true",
         help="Add trailing /1 and /2 for interleaved pairs",
     )
-    p.add_option(
+    p.add_argument(
         "--sequential",
         default=None,
         choices=sequential_choices,
         help="Add sequential IDs",
     )
-    p.add_option(
+    p.add_argument(
         "--sequentialoffset", default=0, type=int, help="Sequential IDs start at"
     )
-    p.add_option(
+    p.add_argument(
         "--pad0", default=0, type=int, help="Pad a few zeros in front of sequential"
     )
-    p.add_option(
+    p.add_argument(
         "--gb",
         default=False,
         action="store_true",
         help="For Genbank ID, get the accession",
     )
-    p.add_option("--sep", default=None, help="Split description by certain symbol")
-    p.add_option(
+    p.add_argument("--sep", default=None, help="Split description by certain symbol")
+    p.add_argument(
         "--index",
         default=0,
         type=int,
         help="Extract i-th field after split with --sep",
     )
-    p.add_option(
+    p.add_argument(
         "--noversion",
         default=False,
         action="store_true",
         help="Remove the gb trailing version",
     )
-    p.add_option("--prefix", help="Prepend prefix to sequence ID")
-    p.add_option("--suffix", help="Append suffix to sequence ID")
-    p.add_option(
+    p.add_argument("--prefix", help="Prepend prefix to sequence ID")
+    p.add_argument("--suffix", help="Append suffix to sequence ID")
+    p.add_argument(
         "--template",
         default=False,
         action="store_true",
         help="Extract `template=aaa dir=x library=m` to `m-aaa/x`",
     )
-    p.add_option("--switch", help="Switch ID from two-column file")
-    p.add_option(
+    p.add_argument("--switch", help="Switch ID from two-column file")
+    p.add_argument(
         "--annotation",
         help="Add functional annotation from two-column file ('ID <--> Annotation')",
     )
-    p.add_option("--ids", help="Generate ID conversion table")
-    p.add_option(
+    p.add_argument("--ids", help="Generate ID conversion table")
+    p.add_argument(
         "--upper",
         default=False,
         action="store_true",
         help="Convert sequence to upper case",
     )
-    p.add_option(
+    p.add_argument(
         "--nodesc",
         default=False,
         action="store_true",
         help="Remove description after identifier",
     )
-    p.add_option(
+    p.add_argument(
         "--minlength", default=0, type=int, help="Minimum sequence length to keep"
     )
     opts, args = p.parse_args(args)
@@ -1522,31 +1526,31 @@ def diff(args):
     from jcvi.utils.table import banner
 
     p = OptionParser(diff.__doc__)
-    p.add_option(
+    p.add_argument(
         "--ignore_case",
         default=False,
         action="store_true",
         help="ignore case when comparing sequences",
     )
-    p.add_option(
+    p.add_argument(
         "--ignore_N",
         default=False,
         action="store_true",
         help="ignore N and X's when comparing sequences",
     )
-    p.add_option(
+    p.add_argument(
         "--ignore_stop",
         default=False,
         action="store_true",
         help="ignore stop codon when comparing sequences",
     )
-    p.add_option(
+    p.add_argument(
         "--rc",
         default=False,
         action="store_true",
         help="also consider reverse complement",
     )
-    p.add_option(
+    p.add_argument(
         "--quiet",
         default=False,
         action="store_true",
@@ -1665,31 +1669,31 @@ def identical(args):
     allowed_checksum = ["MD5", "GCG"]
 
     p = OptionParser(identical.__doc__)
-    p.add_option(
+    p.add_argument(
         "--ignore_case",
         default=False,
         action="store_true",
         help="ignore case when comparing sequences",
     )
-    p.add_option(
+    p.add_argument(
         "--ignore_N",
         default=False,
         action="store_true",
         help="ignore N and X's when comparing sequences",
     )
-    p.add_option(
+    p.add_argument(
         "--ignore_stop",
         default=False,
         action="store_true",
         help="ignore stop codon when comparing sequences",
     )
-    p.add_option(
+    p.add_argument(
         "--output_uniq",
         default=False,
         action="store_true",
         help="output uniq sequences in FASTA format",
     )
-    p.add_option(
+    p.add_argument(
         "--checksum",
         default="MD5",
         choices=allowed_checksum,
@@ -1788,19 +1792,19 @@ def some(args):
     from jcvi.utils.cbook import gene_name
 
     p = OptionParser(some.__doc__)
-    p.add_option(
+    p.add_argument(
         "--exclude",
         default=False,
         action="store_true",
         help="Output sequences not in the list file",
     )
-    p.add_option(
+    p.add_argument(
         "--no_strip_names",
         default=False,
         action="store_true",
         help="Do not strip alternative splicing (e.g. At5g06540.1 -> At5g06540)",
     )
-    p.add_option(
+    p.add_argument(
         "--uniprot", default=False, action="store_true", help="Header is from uniprot"
     )
 
@@ -1863,7 +1867,7 @@ def fastq(args):
     from jcvi.formats.fastq import FastqLite
 
     p = OptionParser(fastq.__doc__)
-    p.add_option("--qv", type=int, help="Use generic qv value")
+    p.add_argument("--qv", type=int, help="Use generic qv value")
 
     opts, args = p.parse_args(args)
 
@@ -1911,7 +1915,7 @@ def pair(args):
         help="Separator in name to reduce to clone id"
         + "e.g. GFNQ33242/1 use /, BOT01-2453H.b1 use .",
     )
-    p.add_option(
+    p.add_argument(
         "-m",
         dest="matepairs",
         default=False,
@@ -1995,7 +1999,7 @@ def pairinplace(args):
     bulk.frags.fasta.
     """
     p = OptionParser(pairinplace.__doc__)
-    p.add_option(
+    p.add_argument(
         "-r",
         dest="rclip",
         default=1,
@@ -2053,23 +2057,23 @@ def extract(args):
     "seqname", or "seqname:start-stop", or "seqname:start-stop:-"
     """
     p = OptionParser(extract.__doc__)
-    p.add_option("--newname", help="Use this new name instead")
-    p.add_option(
+    p.add_argument("--newname", help="Use this new name instead")
+    p.add_argument(
         "--include",
         default=False,
         action="store_true",
         help="search description line for match",
     )
-    p.add_option(
+    p.add_argument(
         "--exclude",
         default=False,
         action="store_true",
         help="exclude description that matches",
     )
-    p.add_option(
+    p.add_argument(
         "--idonly", default=False, action="store_true", help="Only search identifier"
     )
-    p.add_option(
+    p.add_argument(
         "--bed",
         default=None,
         help="path to bed file to guide extraction by matching seqname",
@@ -2197,10 +2201,10 @@ def uniq(args):
     remove fasta records that are the same
     """
     p = OptionParser(uniq.__doc__)
-    p.add_option(
+    p.add_argument(
         "--seq", default=False, action="store_true", help="Uniqify the sequences"
     )
-    p.add_option(
+    p.add_argument(
         "-t",
         "--trimname",
         dest="trimname",
@@ -2314,14 +2318,14 @@ def trim(args):
     from jcvi.algorithms.maxsum import max_sum
 
     p = OptionParser(trim.__doc__)
-    p.add_option(
+    p.add_argument(
         "-c",
         dest="min_length",
         type=int,
         default=64,
         help="minimum sequence length after trimming",
     )
-    p.add_option("-s", dest="score", default=QUAL, help="quality trimming cutoff")
+    p.add_argument("-s", dest="score", default=QUAL, help="quality trimming cutoff")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -2394,12 +2398,12 @@ def sequin(args):
     TATTAACGATGAATAATAATGAGAAGCCATATAGAATTGGTGATAATGTAAAAAAAGGGGCTCTTATTAC
     """
     p = OptionParser(sequin.__doc__)
-    p.add_option("--unk", default=100, type=int, help="The size for unknown gaps")
-    p.add_option("--newid", default=None, help="Use this identifier instead")
-    p.add_option(
+    p.add_argument("--unk", default=100, type=int, help="The size for unknown gaps")
+    p.add_argument("--newid", default=None, help="Use this identifier instead")
+    p.add_argument(
         "--chromosome", default=None, help="Add [chromosome= ] to FASTA header"
     )
-    p.add_option("--clone", default=None, help="Add [clone= ] to FASTA header")
+    p.add_argument("--clone", default=None, help="Add [clone= ] to FASTA header")
     p.set_mingap(default=100)
     opts, args = p.parse_args(args)
 
@@ -2485,14 +2489,14 @@ def tidy(args):
     Trim terminal Ns, normalize gap sizes and remove small components.
     """
     p = OptionParser(tidy.__doc__)
-    p.add_option(
+    p.add_argument(
         "--gapsize",
         dest="gapsize",
         default=0,
         type=int,
         help="Set all gaps to the same size",
     )
-    p.add_option(
+    p.add_argument(
         "--minlen",
         dest="minlen",
         default=100,
@@ -2594,7 +2598,7 @@ def gaps(args):
     from jcvi.formats.agp import mask, build
 
     p = OptionParser(gaps.__doc__)
-    p.add_option(
+    p.add_argument(
         "--split", default=False, action="store_true", help="Generate .split.fasta"
     )
     p.set_mingap(default=100)
diff --git a/jcvi/formats/fastq.py b/jcvi/formats/fastq.py
index ab09bc96..b0141274 100644
--- a/jcvi/formats/fastq.py
+++ b/jcvi/formats/fastq.py
@@ -356,13 +356,13 @@ def readlen(args):
     """
     p = OptionParser(readlen.__doc__)
     p.set_firstN()
-    p.add_option(
+    p.add_argument(
         "--silent",
         default=False,
         action="store_true",
         help="Do not print read length stats",
     )
-    p.add_option(
+    p.add_argument(
         "--nocheck",
         default=False,
         action="store_true",
@@ -392,7 +392,7 @@ def fasta(args):
     Convert fastq to fasta and qual file.
     """
     p = OptionParser(fasta.__doc__)
-    p.add_option(
+    p.add_argument(
         "--seqtk", default=False, action="store_true", help="Use seqtk to convert"
     )
     p.set_outdir()
@@ -496,14 +496,14 @@ def filter(args):
     format (two files) to filter on paired reads.
     """
     p = OptionParser(filter.__doc__)
-    p.add_option(
+    p.add_argument(
         "-q",
         dest="qv",
         default=20,
         type=int,
         help="Minimum quality score to keep",
     )
-    p.add_option(
+    p.add_argument(
         "-p",
         dest="pct",
         default=95,
@@ -709,7 +709,7 @@ def format(args):
     """
     p = OptionParser(format.__doc__)
 
-    p.add_option(
+    p.add_argument(
         "--convert",
         default=None,
         choices=[">=1.8", "<1.8", "sra"],
@@ -784,14 +784,14 @@ def trim(args):
     Wraps `fastx_trimmer` to trim from begin or end of reads.
     """
     p = OptionParser(trim.__doc__)
-    p.add_option(
+    p.add_argument(
         "-f",
         dest="first",
         default=0,
         type=int,
         help="First base to keep. Default is 1.",
     )
-    p.add_option(
+    p.add_argument(
         "-l",
         dest="last",
         default=0,
@@ -861,14 +861,14 @@ def splitread(args):
     Split fastqfile into two read fastqfiles, cut in the middle.
     """
     p = OptionParser(splitread.__doc__)
-    p.add_option(
+    p.add_argument(
         "-n",
         dest="n",
         default=76,
         type=int,
         help="Split at N-th base position",
     )
-    p.add_option(
+    p.add_argument(
         "--rc",
         default=False,
         action="store_true",
@@ -993,7 +993,7 @@ def pairinplace(args):
     p = OptionParser(pairinplace.__doc__)
     p.set_rclip()
     p.set_tag()
-    p.add_option("--base", help="Base name for the output files")
+    p.add_argument("--base", help="Base name for the output files")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -1050,13 +1050,13 @@ def fromsra(args):
     Convert sra file to fastq using the sratoolkit `fastq-dump`
     """
     p = OptionParser(fromsra.__doc__)
-    p.add_option(
+    p.add_argument(
         "--paired",
         default=False,
         action="store_true",
         help="Specify if library layout is paired-end",
     )
-    p.add_option(
+    p.add_argument(
         "--compress",
         default=None,
         choices=["gzip", "bzip2"],
diff --git a/jcvi/formats/genbank.py b/jcvi/formats/genbank.py
index 799b01d3..1b00df60 100644
--- a/jcvi/formats/genbank.py
+++ b/jcvi/formats/genbank.py
@@ -326,23 +326,23 @@ def gff(args):
 
 
 def preparegb(p, args):
-    p.add_option(
+    p.add_argument(
         "--gb_dir", default=None, help="path to dir containing GanBank files (.gb)"
     )
-    p.add_option(
+    p.add_argument(
         "--id",
         default=None,
         help="GenBank accession IDs in a file. One ID per row, or all IDs"
         " in one row comma separated.",
     )
-    p.add_option(
+    p.add_argument(
         "--simple",
         default=None,
         type=str,
         help="GenBank accession IDs comma separated "
         "(for lots of IDs please use --id instead).",
     )
-    p.add_option(
+    p.add_argument(
         "--individual",
         default=False,
         action="store_true",
@@ -388,7 +388,7 @@ def tofasta(args):
     or all records in one file
     """
     p = OptionParser(tofasta.__doc__)
-    p.add_option("--prefix", default="gbfasta", help="prefix of output files")
+    p.add_argument("--prefix", default="gbfasta", help="prefix of output files")
     filenames, accessions, idfile, opts, args = preparegb(p, args)
     prefix = opts.prefix
 
@@ -411,8 +411,8 @@ def getgenes(args):
     Either --gb_dir or --id/--simple should be provided.
     """
     p = OptionParser(getgenes.__doc__)
-    p.add_option("--prefix", default="gbout", help="prefix of output files")
-    p.add_option(
+    p.add_argument("--prefix", default="gbout", help="prefix of output files")
+    p.add_argument(
         "--nopep",
         default=False,
         action="store_true",
@@ -467,14 +467,14 @@ def getquals(args):
     into a tab-delimited file
     """
     p = OptionParser(getquals.__doc__)
-    p.add_option(
+    p.add_argument(
         "--types",
         default="gene,mRNA,CDS",
         type=str,
         dest="quals_ftypes",
         help="Feature types from which to extract qualifiers",
     )
-    p.add_option(
+    p.add_argument(
         "--ignore",
         default="locus_tag,product,codon_start,translation",
         type=str,
diff --git a/jcvi/formats/gff.py b/jcvi/formats/gff.py
index 4259896b..1a47b39f 100644
--- a/jcvi/formats/gff.py
+++ b/jcvi/formats/gff.py
@@ -546,8 +546,8 @@ def addparent(args):
     Merge sister features and infer parents.
     """
     p = OptionParser(addparent.__doc__)
-    p.add_option("--childfeat", default="CDS", help="Type of children feature")
-    p.add_option("--parentfeat", default="mRNA", help="Type of merged feature")
+    p.add_argument("--childfeat", default="CDS", help="Type of children feature")
+    p.add_argument("--parentfeat", default="mRNA", help="Type of merged feature")
     p.set_outfile()
     opts, args = p.parse_args(args)
 
@@ -812,13 +812,13 @@ def sizes(args):
     """
     p = OptionParser(sizes.__doc__)
     p.set_outfile()
-    p.add_option(
+    p.add_argument(
         "--parents",
         dest="parents",
         default="mRNA",
         help="parent feature(s) for which size is to be calculated",
     )
-    p.add_option(
+    p.add_argument(
         "--child",
         dest="child",
         default="CDS",
@@ -861,13 +861,13 @@ def cluster(args):
     from itertools import combinations
 
     p = OptionParser(cluster.__doc__)
-    p.add_option(
+    p.add_argument(
         "--slop",
         default=False,
         action="store_true",
         help="allow minor variation in terminal 5'/3' UTR" + " start/stop position",
     )
-    p.add_option(
+    p.add_argument(
         "--inferUTR",
         default=False,
         action="store_true",
@@ -968,13 +968,13 @@ def summary(args):
     from jcvi.utils.table import tabulate
 
     p = OptionParser(summary.__doc__)
-    p.add_option(
+    p.add_argument(
         "--isoform",
         default=False,
         action="store_true",
         help="Find longest isoform of each id",
     )
-    p.add_option("--ids", help="Only include features from certain IDs")
+    p.add_argument("--ids", help="Only include features from certain IDs")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -1166,23 +1166,23 @@ def filter(args):
     (2) Total bp length of child features
     """
     p = OptionParser(filter.__doc__)
-    p.add_option(
+    p.add_argument(
         "--type", default="mRNA", help="The feature to scan for the attributes"
     )
     g1 = p.add_argument_group("Filter by identity/coverage attribute values")
-    g1.add_option("--id", default=95, type=float, help="Minimum identity")
-    g1.add_option("--coverage", default=90, type=float, help="Minimum coverage")
-    g1.add_option(
+    g1.add_argument("--id", default=95, type=float, help="Minimum identity")
+    g1.add_argument("--coverage", default=90, type=float, help="Minimum coverage")
+    g1.add_argument(
         "--nocase",
         default=False,
         action="store_true",
         help="Case insensitive lookup of attribute names",
     )
     g2 = p.add_argument_group("Filter by child feature bp length")
-    g2.add_option(
+    g2.add_argument(
         "--child_ftype", default=None, type=str, help="Child featuretype to consider"
     )
-    g2.add_option(
+    g2.add_argument(
         "--child_bp",
         default=None,
         type=int,
@@ -1381,35 +1381,35 @@ def chain(args):
     valid_merge_op = ("sum", "min", "max", "mean", "collapse")
 
     p = OptionParser(chain.__doc__)
-    p.add_option(
+    p.add_argument(
         "--key",
         dest="attrib_key",
         default=None,
         help="Attribute to use as `key` for chaining operation",
     )
-    p.add_option(
+    p.add_argument(
         "--chain_ftype",
         default="cDNA_match",
         help="GFF feature type to use for chaining operation",
     )
-    p.add_option(
+    p.add_argument(
         "--parent_ftype",
         default=None,
         help="GFF feature type to use for the chained coordinates",
     )
-    p.add_option(
+    p.add_argument(
         "--break",
         dest="break_chain",
         action="store_true",
         help="Break long chains which are non-contiguous",
     )
-    p.add_option(
+    p.add_argument(
         "--transfer_attrib",
         dest="attrib_list",
         help="Attributes to transfer to parent feature; accepts comma"
         + " separated list of attribute names",
     )
-    p.add_option(
+    p.add_argument(
         "--transfer_score",
         dest="score_merge_op",
         choices=valid_merge_op,
@@ -1547,48 +1547,48 @@ def format(args):
     p = OptionParser(format.__doc__)
 
     g1 = p.add_argument_group("Parameter(s) used to modify GFF attributes (9th column)")
-    g1.add_option("--name", help="Add Name attribute from two-column file")
-    g1.add_option("--note", help="Add Note attribute from two-column file")
-    g1.add_option(
+    g1.add_argument("--name", help="Add Name attribute from two-column file")
+    g1.add_argument("--note", help="Add Note attribute from two-column file")
+    g1.add_argument(
         "--add_attribute",
         dest="attrib_files",
         help="Add new attribute(s) "
         + "from two-column file(s); attribute name comes from filename; "
         + "accepts comma-separated list of files",
     )
-    g1.add_option(
+    g1.add_argument(
         "--add_dbxref",
         dest="dbxref_files",
         help="Add new Dbxref value(s) (DBTAG:ID) "
         + "from two-column file(s). DBTAG comes from filename, ID comes from 2nd column; "
         + "accepts comma-separated list of files",
     )
-    g1.add_option(
+    g1.add_argument(
         "--nostrict",
         default=False,
         action="store_true",
         help="Disable strict parsing of GFF file and/or mapping file",
     )
-    g1.add_option(
+    g1.add_argument(
         "--remove_attr",
         dest="remove_attrs",
         help="Specify attributes to remove; "
         + "accepts comma-separated list of attribute names",
     )
-    g1.add_option(
+    g1.add_argument(
         "--copy_id_attr_to_name",
         default=False,
         action="store_true",
         help="Copy `ID` attribute value to `Name`, when `Name` is not defined",
     )
-    g1.add_option(
+    g1.add_argument(
         "--invent_name_attr",
         default=False,
         action="store_true",
         help="Invent `Name` attribute for 2nd level child features; "
         + "Formatted like PARENT:FEAT_TYPE:FEAT_INDEX",
     )
-    g1.add_option(
+    g1.add_argument(
         "--no_keep_attr_order",
         default=False,
         action="store_true",
@@ -1596,22 +1596,22 @@ def format(args):
     )
 
     g2 = p.add_argument_group("Parameter(s) used to modify content within columns 1-8")
-    g2.add_option(
+    g2.add_argument(
         "--seqid",
         help="Switch seqid from two-column file. If not"
         + " a file, value will globally replace GFF seqid",
     )
-    g2.add_option(
+    g2.add_argument(
         "--source",
         help="Switch GFF source from two-column file. If not"
         + " a file, value will globally replace GFF source",
     )
-    g2.add_option(
+    g2.add_argument(
         "--type",
         help="Switch GFF feature type from two-column file. If not"
         + " a file, value will globally replace GFF type",
     )
-    g2.add_option(
+    g2.add_argument(
         "--fixphase",
         default=False,
         action="store_true",
@@ -1621,53 +1621,53 @@ def format(args):
     g3 = p.add_argument_group(
         "Other parameter(s) to perform manipulations to the GFF file content"
     )
-    g3.add_option(
+    g3.add_argument(
         "--unique", default=False, action="store_true", help="Make IDs unique"
     )
-    g3.add_option(
+    g3.add_argument(
         "--chaindup",
         default=None,
         dest="duptype",
         help="Chain duplicate features of a particular GFF3 `type`,"
         + " sharing the same ID attribute",
     )
-    g3.add_option(
+    g3.add_argument(
         "--multiparents",
         default=None,
         choices=valid_multiparent_ops,
         help="Split/merge identical features (same `seqid`, `source`, `type`, `coord-range`, `strand`, `phase`) mapping to multiple parents",
     )
-    g3.add_option(
+    g3.add_argument(
         "--remove_feats", help="Comma separated list of features to remove by type"
     )
-    g3.add_option(
+    g3.add_argument(
         "--remove_feats_by_ID",
         help="List of features to remove by ID;"
         + " accepts comma-separated list or list file",
     )
-    g3.add_option(
+    g3.add_argument(
         "--gsac",
         default=False,
         action="store_true",
         help="Fix GSAC GFF3 file attributes",
     )
-    g3.add_option(
+    g3.add_argument(
         "--invent_protein_feat",
         default=False,
         action="store_true",
         help="Invent a protein feature span (chain CDS feats)",
     )
-    g3.add_option(
+    g3.add_argument(
         "--process_ftype",
         default=None,
         type=str,
         help="Specify feature types to process; "
         "accepts comma-separated list of feature types",
     )
-    g3.add_option(
+    g3.add_argument(
         "--gff3", default=False, action="store_true", help="Print output in GFF3 format"
     )
-    g3.add_option(
+    g3.add_argument(
         "--make_gff_store",
         default=False,
         action="store_true",
@@ -2057,13 +2057,13 @@ def fixboundaries(args):
     range chained child features, extracting their min and max values
     """
     p = OptionParser(fixboundaries.__doc__)
-    p.add_option(
+    p.add_argument(
         "--type",
         default="gene",
         type=str,
         help="Feature type for which to adjust boundaries",
     )
-    p.add_option(
+    p.add_argument(
         "--child_ftype",
         default="mRNA",
         type=str,
@@ -2101,7 +2101,7 @@ def liftover(args):
     "gannotation.asmbl.000095.7" is the 8-th tile on asmbl.000095.
     """
     p = OptionParser(liftover.__doc__)
-    p.add_option("--tilesize", default=50000, type=int, help="The size for each tile")
+    p.add_argument("--tilesize", default=50000, type=int, help="The size for each tile")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -2252,16 +2252,16 @@ def uniq(args):
     """
     supported_modes = ("span", "score")
     p = OptionParser(uniq.__doc__)
-    p.add_option("--type", default="gene", help="Types of features to non-redundify")
-    p.add_option("--mode", default="span", choices=supported_modes, help="Pile mode")
-    p.add_option("--best", default=1, type=int, help="Use best N features")
-    p.add_option(
+    p.add_argument("--type", default="gene", help="Types of features to non-redundify")
+    p.add_argument("--mode", default="span", choices=supported_modes, help="Pile mode")
+    p.add_argument("--best", default=1, type=int, help="Use best N features")
+    p.add_argument(
         "--name",
         default=False,
         action="store_true",
         help="Non-redundify Name attribute",
     )
-    p.add_option(
+    p.add_argument(
         "--iter",
         default="2",
         choices=("1", "2"),
@@ -2370,13 +2370,13 @@ def sort(args):
     valid_sort_methods = ("unix", "topo")
 
     p = OptionParser(sort.__doc__)
-    p.add_option(
+    p.add_argument(
         "--method",
         default="unix",
         choices=valid_sort_methods,
         help="Specify sort method",
     )
-    p.add_option(
+    p.add_argument(
         "-i",
         dest="inplace",
         default=False,
@@ -2430,11 +2430,11 @@ def fromgtf(args):
     the "transcript_id" in exon/CDS feature will be converted to "Parent=".
     """
     p = OptionParser(fromgtf.__doc__)
-    p.add_option(
+    p.add_argument(
         "--transcript_id", default="transcript_id", help="Field name for transcript"
     )
-    p.add_option("--gene_id", default="gene_id", help="Field name for gene")
-    p.add_option(
+    p.add_argument("--gene_id", default="gene_id", help="Field name for gene")
+    p.add_argument(
         "--augustus", default=False, action="store_true", help="Input is AUGUSTUS gtf"
     )
     p.set_home("augustus")
@@ -2489,8 +2489,8 @@ def frombed(args):
     Default type will be `match` and default source will be `source`
     """
     p = OptionParser(frombed.__doc__)
-    p.add_option("--type", default="match", help="GFF feature type")
-    p.add_option("--source", default="default", help="GFF source qualifier")
+    p.add_argument("--type", default="match", help="GFF feature type")
+    p.add_argument("--source", default="default", help="GFF source qualifier")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -2509,8 +2509,8 @@ def fromsoap(args):
 
     """
     p = OptionParser(fromsoap.__doc__)
-    p.add_option("--type", default="nucleotide_match", help="GFF feature type")
-    p.add_option("--source", default="soap", help="GFF source qualifier")
+    p.add_argument("--type", default="nucleotide_match", help="GFF feature type")
+    p.add_argument("--source", default="soap", help="GFF source qualifier")
     p.set_fixchrnames(orgn="maize")
     p.set_outfile()
     opts, args = p.parse_args(args)
@@ -2617,7 +2617,7 @@ def merge(args):
     to be a file with a list of gff files.
     """
     p = OptionParser(merge.__doc__)
-    p.add_option(
+    p.add_argument(
         "--seq",
         default=False,
         action="store_true",
@@ -2685,23 +2685,23 @@ def extract(args):
     involved, use "," to separate; or provide a file with multiple IDs, one per line
     """
     p = OptionParser(extract.__doc__)
-    p.add_option("--contigs", help="Extract features from certain contigs")
-    p.add_option("--names", help="Extract features with certain names")
-    p.add_option(
+    p.add_argument("--contigs", help="Extract features from certain contigs")
+    p.add_argument("--names", help="Extract features with certain names")
+    p.add_argument(
         "--types",
         type=str,
         default=None,
         help="Extract features of certain feature types",
     )
-    p.add_option(
+    p.add_argument(
         "--children",
         default=0,
         choices=["1", "2"],
         help="Specify number of iterations: `1` grabs children, "
         + "`2` grabs grand-children",
     )
-    p.add_option("--tag", default="ID", help="Scan the tags for the names")
-    p.add_option(
+    p.add_argument("--tag", default="ID", help="Scan the tags for the names")
+    p.add_argument(
         "--fasta", default=False, action="store_true", help="Write FASTA if available"
     )
     p.set_outfile()
@@ -2802,18 +2802,18 @@ def note(args):
     Extract certain attribute field for each feature.
     """
     p = OptionParser(note.__doc__)
-    p.add_option(
+    p.add_argument(
         "--type",
         default=None,
         help="Only process certain types, multiple types allowed with comma",
     )
-    p.add_option(
+    p.add_argument(
         "--attribute",
         default="Parent,Note",
         help="Attribute field to extract, multiple fields allowd with comma",
     )
-    p.add_option("--AED", type=float, help="Only extract lines with AED score <=")
-    p.add_option(
+    p.add_argument("--AED", type=float, help="Only extract lines with AED score <=")
+    p.add_argument(
         "--exoncount",
         default=False,
         action="store_true",
@@ -2955,68 +2955,68 @@ def bed(args):
     generate a bed file
     """
     p = OptionParser(bed.__doc__)
-    p.add_option(
+    p.add_argument(
         "--type",
         dest="type",
         default="gene",
         help="Feature type to extract, use comma for multiple, and `all` for all",
     )
-    p.add_option("--key", default="ID", help="Key in the attributes to extract")
-    p.add_option("--accn", help="Use fixed accn in the 4th column")
-    p.add_option("--source", help="Source to extract from, use comma for multiple")
-    p.add_option(
+    p.add_argument("--key", default="ID", help="Key in the attributes to extract")
+    p.add_argument("--accn", help="Use fixed accn in the 4th column")
+    p.add_argument("--source", help="Source to extract from, use comma for multiple")
+    p.add_argument(
         "--span",
         default=False,
         action="store_true",
         help="Use feature span in the score column",
     )
-    p.add_option(
+    p.add_argument(
         "--score_attrib",
         dest="score_attrib",
         default=False,
         help="Attribute whose value is to be used as score in `bedline`",
     )
-    p.add_option(
+    p.add_argument(
         "--append_source",
         default=False,
         action="store_true",
         help="Append GFF source name to extracted key value",
     )
-    p.add_option(
+    p.add_argument(
         "--append_ftype",
         default=False,
         action="store_true",
         help="Append GFF feature type to extracted key value",
     )
-    p.add_option(
+    p.add_argument(
         "--append_attrib",
         default=None,
         help="Append attribute to extracted key value",
     )
-    p.add_option(
+    p.add_argument(
         "--nosort",
         default=False,
         action="store_true",
         help="Do not sort the output bed file",
     )
-    p.add_option(
+    p.add_argument(
         "--primary_only",
         default=False,
         action="store_true",
         help="Only retains a single transcript per gene",
     )
-    p.add_option(
+    p.add_argument(
         "--parent_key",
         default="Parent",
         help="Parent gene key to group with --primary_only",
     )
-    p.add_option(
+    p.add_argument(
         "--human_chr",
         default=False,
         action="store_true",
         help="Only allow 1-22XY, and add `chr` prefix to seqid",
     )
-    p.add_option(
+    p.add_argument(
         "--ensembl_cds",
         default=False,
         action="store_true",
@@ -3145,7 +3145,7 @@ def children(args):
     Get the children that have the same parent.
     """
     p = OptionParser(children.__doc__)
-    p.add_option(
+    p.add_argument(
         "--parents",
         default="gene",
         help="list of features to extract, use comma to separate (e.g. 'gene,mRNA')",
@@ -3199,21 +3199,21 @@ def load(args):
     valid_avoid_features = ["both_strands", "strand_specific"]
 
     p = OptionParser(load.__doc__)
-    p.add_option(
+    p.add_argument(
         "--parents",
         dest="parents",
         default="mRNA",
         help="list of features to extract, use comma to separate (e.g."
         + "'gene,mRNA')",
     )
-    p.add_option(
+    p.add_argument(
         "--children",
         dest="children",
         default="CDS",
         help="list of features to extract, use comma to separate (e.g."
         + "'five_prime_UTR,CDS,three_prime_UTR')",
     )
-    p.add_option(
+    p.add_argument(
         "--feature",
         dest="feature",
         help="feature type to extract (e.g. `--feature=CDS`). Extract "
@@ -3221,23 +3221,23 @@ def load(args):
         + "upstream|downstream:TSS|TrSS|TES|TrES:length "
         + "(e.g. `--feature=upstream:TSS:500`)",
     )
-    p.add_option(
+    p.add_argument(
         "--avoidFeatures",
         default=None,
         choices=["both_strands", "strand_specific"],
         help="Specify whether or not to avoid up or downstream features",
     )
-    p.add_option(
+    p.add_argument(
         "--id_attribute",
         choices=valid_id_attributes,
         help="The attribute field to extract and use as FASTA sequence ID",
     )
-    p.add_option(
+    p.add_argument(
         "--desc_attribute",
         default="Note",
         help="The attribute field to extract and use as FASTA sequence description",
     )
-    p.add_option(
+    p.add_argument(
         "--full_header",
         default=None,
         choices=["default", "tair"],
@@ -3245,18 +3245,18 @@ def load(args):
     )
 
     g1 = p.add_argument_group("Optional parameters (if generating full header)")
-    g1.add_option(
+    g1.add_argument(
         "--sep",
         dest="sep",
         default=" ",
         help="Specify separator used to delimiter header elements",
     )
-    g1.add_option(
+    g1.add_argument(
         "--datestamp",
         dest="datestamp",
         help="Specify a datestamp in the format YYYYMMDD or automatically pick `today`",
     )
-    g1.add_option(
+    g1.add_argument(
         "--conf_class",
         dest="conf_class",
         default=False,
@@ -3693,9 +3693,9 @@ def bed12(args):
     12. blockStarts
     """
     p = OptionParser(bed12.__doc__)
-    p.add_option("--parent", default="mRNA", help="Top feature type")
-    p.add_option("--block", default="exon", help="Feature type for regular blocks")
-    p.add_option("--thick", default="CDS", help="Feature type for thick blocks")
+    p.add_argument("--parent", default="mRNA", help="Top feature type")
+    p.add_argument("--block", default="exon", help="Feature type for regular blocks")
+    p.add_argument("--thick", default="CDS", help="Feature type for thick blocks")
     p.set_outfile()
     opts, args = p.parse_args(args)
 
diff --git a/jcvi/formats/html.py b/jcvi/formats/html.py
index 632259d1..9891e0bb 100644
--- a/jcvi/formats/html.py
+++ b/jcvi/formats/html.py
@@ -40,8 +40,8 @@ def gallery(args):
     from jcvi.apps.base import iglob
 
     p = OptionParser(gallery.__doc__)
-    p.add_option("--columns", default=3, type=int, help="How many cells per row")
-    p.add_option("--width", default=200, type=int, help="Image width")
+    p.add_argument("--columns", default=3, type=int, help="How many cells per row")
+    p.add_argument("--width", default=200, type=int, help="Image width")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -72,7 +72,7 @@ def links(args):
     Extract all the links "<a href=''>" from web page.
     """
     p = OptionParser(links.__doc__)
-    p.add_option(
+    p.add_argument(
         "--img",
         default=False,
         action="store_true",
diff --git a/jcvi/formats/obo.py b/jcvi/formats/obo.py
index 4ac9c6ae..7b2d4d51 100755
--- a/jcvi/formats/obo.py
+++ b/jcvi/formats/obo.py
@@ -74,7 +74,7 @@ def validate_term(term, so=None, method="verify"):
 
 if __name__ == "__main__":
     p = OptionParser(__doc__)
-    p.add_option(
+    p.add_argument(
         "--term",
         help="Write the parents and children of this query term",
     )
diff --git a/jcvi/formats/paf.py b/jcvi/formats/paf.py
index a7f3087b..cb4a7277 100644
--- a/jcvi/formats/paf.py
+++ b/jcvi/formats/paf.py
@@ -90,7 +90,7 @@ def bed(args):
     from jcvi.formats.bed import sort as sort_bed
 
     p = OptionParser(bed.__doc__)
-    p.add_option(
+    p.add_argument(
         "--swap", default=False, action="store_true", help="Write query positions"
     )
 
diff --git a/jcvi/formats/pdf.py b/jcvi/formats/pdf.py
index 5160dca5..1be1b381 100644
--- a/jcvi/formats/pdf.py
+++ b/jcvi/formats/pdf.py
@@ -47,10 +47,10 @@ def cat(args):
             In case you don't want chapter 10 before chapter 2.
     """
     p = OptionParser(cat.__doc__.format(page_range_help=PAGE_RANGE_HELP))
-    p.add_option(
+    p.add_argument(
         "--nosort", default=False, action="store_true", help="Do not sort file names"
     )
-    p.add_option(
+    p.add_argument(
         "--cleanup",
         default=False,
         action="store_true",
diff --git a/jcvi/formats/psl.py b/jcvi/formats/psl.py
index 61bb3f6d..c105bd9b 100755
--- a/jcvi/formats/psl.py
+++ b/jcvi/formats/psl.py
@@ -312,20 +312,20 @@ def gff(args):
     Convert to gff format.
     """
     p = OptionParser(gff.__doc__)
-    p.add_option("--source", default="GMAP", help="specify GFF source")
-    p.add_option(
+    p.add_argument("--source", default="GMAP", help="specify GFF source")
+    p.add_argument(
         "--type",
         default="EST_match",
         help="specify GFF feature type",
     )
-    p.add_option("--suffix", default=".match", help="match ID suffix")
-    p.add_option(
+    p.add_argument("--suffix", default=".match", help="match ID suffix")
+    p.add_argument(
         "--swap",
         default=False,
         action="store_true",
         help="swap query and target features",
     )
-    p.add_option(
+    p.add_argument(
         "--simple_score",
         default=False,
         action="store_true",
diff --git a/jcvi/formats/sam.py b/jcvi/formats/sam.py
index 101879f6..c1edcee6 100644
--- a/jcvi/formats/sam.py
+++ b/jcvi/formats/sam.py
@@ -310,7 +310,7 @@ def append(args):
     training AUGUSTUS gene models.
     """
     p = OptionParser(append.__doc__)
-    p.add_option("--prepend", help="Prepend string to read names")
+    p.add_argument("--prepend", help="Prepend string to read names")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -407,7 +407,7 @@ def count(args):
     Count the number of reads mapped using `htseq-count`.
     """
     p = OptionParser(count.__doc__)
-    p.add_option("--type", default="exon", help="Only count feature type")
+    p.add_argument("--type", default="exon", help="Only count feature type")
     p.set_cpus(cpus=8)
     opts, args = p.parse_args(args)
 
@@ -444,13 +444,15 @@ def coverage(args):
     --nosort.
     """
     p = OptionParser(coverage.__doc__)
-    p.add_option(
+    p.add_argument(
         "--format",
         default="bigwig",
         choices=("bedgraph", "bigwig", "coverage"),
         help="Output format",
     )
-    p.add_option("--nosort", default=False, action="store_true", help="Do not sort BAM")
+    p.add_argument(
+        "--nosort", default=False, action="store_true", help="Do not sort BAM"
+    )
     p.set_outfile()
     opts, args = p.parse_args(args)
 
@@ -568,10 +570,10 @@ def consensus(args):
     """
     valid_callers = ("bcftools", "gatk4")
     p = OptionParser(consensus.__doc__)
-    p.add_option(
+    p.add_argument(
         "--nosort", default=False, action="store_true", help="Do not sort the BAM files"
     )
-    p.add_option(
+    p.add_argument(
         "--caller",
         default="bcftools",
         choices=valid_callers,
@@ -610,10 +612,10 @@ def vcf(args):
     valid_callers = ("mpileup", "freebayes")
     p = OptionParser(vcf.__doc__)
     p.set_outfile(outfile="out.vcf.gz")
-    p.add_option(
+    p.add_argument(
         "--nosort", default=False, action="store_true", help="Do not sort the BAM files"
     )
-    p.add_option(
+    p.add_argument(
         "--caller", default="mpileup", choices=valid_callers, help="Use variant caller"
     )
     opts, args = p.parse_args(args)
@@ -704,10 +706,10 @@ def index(args):
     If SAM file, convert to BAM, sort and then index, using SAMTOOLS
     """
     p = OptionParser(index.__doc__)
-    p.add_option(
+    p.add_argument(
         "--fasta", dest="fasta", default=None, help="add @SQ header to the BAM file"
     )
-    p.add_option(
+    p.add_argument(
         "--unique",
         default=False,
         action="store_true",
@@ -887,39 +889,39 @@ def ace(args):
     assembler.
     """
     p = OptionParser(ace.__doc__)
-    p.add_option(
+    p.add_argument(
         "--splitdir",
         dest="splitdir",
         default="outRoot",
         help="split the ace per contig to dir",
     )
-    p.add_option(
+    p.add_argument(
         "--unpaired",
         dest="unpaired",
         default=False,
         help="remove read pairs on the same contig",
     )
-    p.add_option(
+    p.add_argument(
         "--minreadno",
         dest="minreadno",
         default=3,
         type=int,
         help="minimum read numbers per contig",
     )
-    p.add_option(
+    p.add_argument(
         "--minctgsize",
         dest="minctgsize",
         default=100,
         type=int,
         help="minimum contig size per contig",
     )
-    p.add_option(
+    p.add_argument(
         "--astat",
         default=False,
         action="store_true",
         help="create .astat to list repetitiveness",
     )
-    p.add_option(
+    p.add_argument(
         "--readids",
         default=False,
         action="store_true",
diff --git a/jcvi/formats/sizes.py b/jcvi/formats/sizes.py
index b6b5124d..122013ff 100644
--- a/jcvi/formats/sizes.py
+++ b/jcvi/formats/sizes.py
@@ -156,8 +156,8 @@ def histogram(args):
     p.set_histogram(
         vmax=50000, bins=100, xlabel="Read length", title="Read length distribution"
     )
-    p.add_option("--ylabel1", default="Counts", help="Label of y-axis on the left")
-    p.add_option(
+    p.add_argument("--ylabel1", default="Counts", help="Label of y-axis on the left")
+    p.add_argument(
         "--color",
         default="0",
         choices=[str(x) for x in range(8)],
diff --git a/jcvi/formats/vcf.py b/jcvi/formats/vcf.py
index d8e17c6d..3455cfe0 100644
--- a/jcvi/formats/vcf.py
+++ b/jcvi/formats/vcf.py
@@ -151,7 +151,7 @@ def validate(args):
     import pyfasta
 
     p = OptionParser(validate.__doc__)
-    p.add_option("--prefix", help="Add prefix to seqid")
+    p.add_argument("--prefix", help="Add prefix to seqid")
     opts, args = p.parse_args(args)
 
     vcffile, fastafile = args
@@ -496,7 +496,7 @@ def location(args):
     from jcvi.graphics.histogram import stem_leaf_plot
 
     p = OptionParser(location.__doc__)
-    p.add_option(
+    p.add_argument(
         "--dist",
         default=100,
         type=int,
@@ -551,8 +551,8 @@ def summary(args):
     from jcvi.utils.table import tabulate
 
     p = OptionParser(summary.__doc__)
-    p.add_option("--counts", help="Print SNP counts in a txt file")
-    p.add_option("--bed", help="Print SNPs locations in a bed file")
+    p.add_argument("--counts", help="Print SNP counts in a txt file")
+    p.add_argument("--bed", help="Print SNPs locations in a bed file")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -685,43 +685,43 @@ def mstmap(args):
     from jcvi.assembly.geneticmap import MSTMatrix
 
     p = OptionParser(mstmap.__doc__)
-    p.add_option(
+    p.add_argument(
         "--dh",
         default=False,
         action="store_true",
         help="Double haploid population, no het",
     )
-    p.add_option(
+    p.add_argument(
         "--freq",
         default=0.2,
         type=float,
         help="Allele must be above frequency",
     )
-    p.add_option(
+    p.add_argument(
         "--mindepth",
         default=3,
         type=int,
         help="Only trust genotype calls with depth",
     )
-    p.add_option(
+    p.add_argument(
         "--missing_threshold",
         default=0.25,
         type=float,
         help="Fraction missing must be below",
     )
-    p.add_option(
+    p.add_argument(
         "--noheader",
         default=False,
         action="store_true",
         help="Do not print MSTmap run parameters",
     )
-    p.add_option(
+    p.add_argument(
         "--pv4",
         default=False,
         action="store_true",
         help="Enable filtering strand-bias, tail distance bias, etc.",
     )
-    p.add_option(
+    p.add_argument(
         "--freebayes",
         default=False,
         action="store_true",
@@ -796,7 +796,7 @@ def liftover(args):
     Lift over coordinates in vcf file.
     """
     p = OptionParser(liftover.__doc__)
-    p.add_option(
+    p.add_argument(
         "--newid", default=False, action="store_true", help="Make new identifiers"
     )
     opts, args = p.parse_args(args)
diff --git a/jcvi/graphics/assembly.py b/jcvi/graphics/assembly.py
index 50b8d410..264a3e5b 100644
--- a/jcvi/graphics/assembly.py
+++ b/jcvi/graphics/assembly.py
@@ -44,10 +44,10 @@ def covlen(args):
     from jcvi.formats.base import DictFile
 
     p = OptionParser(covlen.__doc__)
-    p.add_option("--maxsize", default=1000000, type=int, help="Max contig size")
-    p.add_option("--maxcov", default=100, type=int, help="Max contig size")
-    p.add_option("--color", default="m", help="Color of the data points")
-    p.add_option(
+    p.add_argument("--maxsize", default=1000000, type=int, help="Max contig size")
+    p.add_argument("--maxcov", default=100, type=int, help="Max contig size")
+    p.add_argument("--color", default="m", help="Color of the data points")
+    p.add_argument(
         "--kind",
         default="scatter",
         choices=("scatter", "reg", "resid", "kde", "hex"),
@@ -109,8 +109,8 @@ def coverage(args):
     from jcvi.formats.bed import mates, bedpe
 
     p = OptionParser(coverage.__doc__)
-    p.add_option("--ymax", default=None, type=int, help="Limit ymax")
-    p.add_option(
+    p.add_argument("--ymax", default=None, type=int, help="Limit ymax")
+    p.add_argument(
         "--spans",
         default=False,
         action="store_true",
@@ -260,13 +260,13 @@ def scaffold(args):
     from more_itertools import grouper
 
     p = OptionParser(scaffold.__doc__)
-    p.add_option(
+    p.add_argument(
         "--cutoff",
         type=int,
         default=1000000,
         help="Plot scaffolds with size larger than",
     )
-    p.add_option(
+    p.add_argument(
         "--highlights",
         help="A set of regions in BED format to highlight",
     )
@@ -450,20 +450,20 @@ def A50(args):
     Plots A50 graphics, see blog post (http://blog.malde.org/index.php/a50/)
     """
     p = OptionParser(A50.__doc__)
-    p.add_option(
+    p.add_argument(
         "--overwrite",
         default=False,
         action="store_true",
         help="overwrite .rplot file if exists",
     )
-    p.add_option(
+    p.add_argument(
         "--cutoff",
         default=0,
         type=int,
         dest="cutoff",
         help="use contigs above certain size",
     )
-    p.add_option(
+    p.add_argument(
         "--stepsize",
         default=10,
         type=int,
diff --git a/jcvi/graphics/blastplot.py b/jcvi/graphics/blastplot.py
index 8f425728..9f98093e 100755
--- a/jcvi/graphics/blastplot.py
+++ b/jcvi/graphics/blastplot.py
@@ -233,43 +233,43 @@ def increaseDensity(a, ratio=4):
     from jcvi.formats.bed import sizes
 
     p = OptionParser(__doc__)
-    p.add_option("--qsizes", help="Path to two column qsizes file")
-    p.add_option("--ssizes", help="Path to two column ssizes file")
-    p.add_option("--qbed", help="Path to qbed")
-    p.add_option("--sbed", help="Path to sbed")
-    p.add_option(
+    p.add_argument("--qsizes", help="Path to two column qsizes file")
+    p.add_argument("--ssizes", help="Path to two column ssizes file")
+    p.add_argument("--qbed", help="Path to qbed")
+    p.add_argument("--sbed", help="Path to sbed")
+    p.add_argument(
         "--qselect",
         default=0,
         type=int,
         help="Minimum size of query contigs to select",
     )
-    p.add_option(
+    p.add_argument(
         "--sselect",
         default=0,
         type=int,
         help="Minimum size of subject contigs to select",
     )
-    p.add_option("--qh", help="Path to highlight bed for query")
-    p.add_option("--sh", help="Path to highlight bed for subject")
-    p.add_option(
+    p.add_argument("--qh", help="Path to highlight bed for query")
+    p.add_argument("--sh", help="Path to highlight bed for subject")
+    p.add_argument(
         "--dotstyle",
         default="dot",
         choices=DotStyles,
         help="Style of the dots",
     )
-    p.add_option(
+    p.add_argument(
         "--proportional",
         default=False,
         action="store_true",
         help="Make image width:height equal to seq ratio",
     )
-    p.add_option(
+    p.add_argument(
         "--stripNames",
         default=False,
         action="store_true",
         help="Remove trailing .? from gene names",
     )
-    p.add_option(
+    p.add_argument(
         "--nmax",
         default=None,
         type=int,
diff --git a/jcvi/graphics/coverage.py b/jcvi/graphics/coverage.py
index 715abd78..69ab792b 100644
--- a/jcvi/graphics/coverage.py
+++ b/jcvi/graphics/coverage.py
@@ -215,7 +215,7 @@ def setup_gauge_ax(gauge_ax, start, end, gauge_step, float_formatter=False):
 
 def main():
     p = OptionParser(__doc__)
-    p.add_option("--order", help="The order to plot the tracks, comma-separated")
+    p.add_argument("--order", help="The order to plot the tracks, comma-separated")
     opts, args, iopts = p.set_image_options()
 
     if len(args) != 3:
diff --git a/jcvi/graphics/dotplot.py b/jcvi/graphics/dotplot.py
index b730a8a2..9bc7a712 100755
--- a/jcvi/graphics/dotplot.py
+++ b/jcvi/graphics/dotplot.py
@@ -400,57 +400,57 @@ def subset_bed(bed, seqids):
 def dotplot_main(args):
     p = OptionParser(__doc__)
     p.set_beds()
-    p.add_option(
+    p.add_argument(
         "--synteny",
         default=False,
         action="store_true",
         help="Run a fast synteny scan and display blocks",
     )
-    p.add_option("--cmaptext", help="Draw colormap box on the bottom-left corner")
-    p.add_option(
+    p.add_argument("--cmaptext", help="Draw colormap box on the bottom-left corner")
+    p.add_argument(
         "--vmin",
         dest="vmin",
         type=float,
         default=0,
         help="Minimum value in the colormap",
     )
-    p.add_option(
+    p.add_argument(
         "--vmax",
         dest="vmax",
         type=float,
         default=2,
         help="Maximum value in the colormap",
     )
-    p.add_option(
+    p.add_argument(
         "--nmax",
         dest="sample_number",
         type=int,
         default=10000,
         help="Maximum number of data points to plot",
     )
-    p.add_option(
+    p.add_argument(
         "--minfont",
         type=int,
         default=4,
         help="Do not render labels with size smaller than",
     )
-    p.add_option("--colormap", help="Two column file, block id to color mapping")
-    p.add_option(
+    p.add_argument("--colormap", help="Two column file, block id to color mapping")
+    p.add_argument(
         "--colororientation",
         action="store_true",
         default=False,
         help="Color the blocks based on orientation, similar to mummerplot",
     )
-    p.add_option(
+    p.add_argument(
         "--nosort",
         default=False,
         action="store_true",
         help="Do not sort the seqids along the axes",
     )
-    p.add_option(
+    p.add_argument(
         "--nosep", default=False, action="store_true", help="Do not add contig lines"
     )
-    p.add_option("--title", help="Title of the dot plot")
+    p.add_argument("--title", help="Title of the dot plot")
     p.set_dotplot_opts()
     p.set_outfile(outfile=None)
     opts, args, iopts = p.set_image_options(
diff --git a/jcvi/graphics/glyph.py b/jcvi/graphics/glyph.py
index 85dd648b..16970ba9 100644
--- a/jcvi/graphics/glyph.py
+++ b/jcvi/graphics/glyph.py
@@ -601,10 +601,12 @@ def gff(args):
     """
     align_choices = ("left", "center", "right")
     p = OptionParser(gff.__doc__)
-    p.add_option(
+    p.add_argument(
         "--align", default="left", choices=align_choices, help="Horizontal alignment"
     )
-    p.add_option("--noUTR", default=False, action="store_true", help="Do not plot UTRs")
+    p.add_argument(
+        "--noUTR", default=False, action="store_true", help="Do not plot UTRs"
+    )
     opts, args = p.parse_args(args)
 
     if len(args) < 1:
diff --git a/jcvi/graphics/grabseeds.py b/jcvi/graphics/grabseeds.py
index 310bd8f0..f9a00e93 100644
--- a/jcvi/graphics/grabseeds.py
+++ b/jcvi/graphics/grabseeds.py
@@ -268,17 +268,17 @@ def add_seeds_options(p, args):
     Add options to the OptionParser for seeds() and batchseeds() functions.
     """
     g1 = p.add_argument_group("Image manipulation")
-    g1.add_option("--rotate", default=0, type=int, help="Rotate degrees clockwise")
-    g1.add_option(
+    g1.add_argument("--rotate", default=0, type=int, help="Rotate degrees clockwise")
+    g1.add_argument(
         "--rows", default=":", help="Crop rows e.g. `:800` from first 800 rows"
     )
-    g1.add_option(
+    g1.add_argument(
         "--cols", default=":", help="Crop cols e.g. `-800:` from last 800 cols"
     )
-    g1.add_option("--labelrows", help="Label rows e.g. `:800` from first 800 rows")
-    g1.add_option("--labelcols", help="Label cols e.g. `-800: from last 800 rows")
+    g1.add_argument("--labelrows", help="Label rows e.g. `:800` from first 800 rows")
+    g1.add_argument("--labelcols", help="Label cols e.g. `-800: from last 800 rows")
     valid_colors = ("red", "green", "blue", "purple", "yellow", "orange", "INVERSE")
-    g1.add_option(
+    g1.add_argument(
         "--changeBackground",
         default=0,
         choices=valid_colors,
@@ -286,17 +286,19 @@ def add_seeds_options(p, args):
     )
 
     g2 = p.add_argument_group("Object recognition")
-    g2.add_option(
+    g2.add_argument(
         "--minsize",
         default=0.05,
         type=float,
         help="Min percentage of object to image",
     )
-    g2.add_option(
+    g2.add_argument(
         "--maxsize", default=50, type=float, help="Max percentage of object to image"
     )
-    g2.add_option("--count", default=100, type=int, help="Report max number of objects")
-    g2.add_option(
+    g2.add_argument(
+        "--count", default=100, type=int, help="Report max number of objects"
+    )
+    g2.add_argument(
         "--watershed",
         default=False,
         action="store_true",
@@ -305,41 +307,41 @@ def add_seeds_options(p, args):
 
     g3 = p.add_argument_group("De-noise")
     valid_filters = ("canny", "roberts", "sobel")
-    g3.add_option(
+    g3.add_argument(
         "--filter",
         default="canny",
         choices=valid_filters,
         help="Edge detection algorithm",
     )
-    g3.add_option(
+    g3.add_argument(
         "--sigma",
         default=1,
         type=int,
         help="Canny edge detection sigma, higher for noisy image",
     )
-    g3.add_option(
+    g3.add_argument(
         "--kernel",
         default=2,
         type=int,
         help="Edge closure, higher if the object edges are dull",
     )
-    g3.add_option(
+    g3.add_argument(
         "--border", default=5, type=int, help="Remove image border of certain pixels"
     )
 
     g4 = p.add_argument_group("Output")
-    g4.add_option("--calibrate", help="JSON file to correct distance and color")
-    g4.add_option(
+    g4.add_argument("--calibrate", help="JSON file to correct distance and color")
+    g4.add_argument(
         "--edges",
         default=False,
         action="store_true",
         help="Visualize edges in middle PDF panel",
     )
-    g4.add_option(
+    g4.add_argument(
         "--outdir", default=".", help="Store intermediate images and PDF in folder"
     )
-    g4.add_option("--prefix", help="Output prefix")
-    g4.add_option(
+    g4.add_argument("--prefix", help="Output prefix")
+    g4.add_argument(
         "--noheader", default=False, action="store_true", help="Do not print header"
     )
     opts, args, iopts = p.set_image_options(args, figsize="12x6", style="white")
diff --git a/jcvi/graphics/heatmap.py b/jcvi/graphics/heatmap.py
index 3f8c1679..200526f0 100644
--- a/jcvi/graphics/heatmap.py
+++ b/jcvi/graphics/heatmap.py
@@ -62,14 +62,14 @@ def parse_csv(csvfile, vmin=0, groups=False):
 
 def main():
     p = OptionParser(__doc__)
-    p.add_option(
+    p.add_argument(
         "--groups",
         default=False,
         action="store_true",
         help="The first row contains group info",
     )
-    p.add_option("--rowgroups", help="Row groupings")
-    p.add_option(
+    p.add_argument("--rowgroups", help="Row groupings")
+    p.add_argument(
         "--horizontalbar",
         default=False,
         action="store_true",
diff --git a/jcvi/graphics/histogram.py b/jcvi/graphics/histogram.py
index cfd226b7..56a5f5af 100644
--- a/jcvi/graphics/histogram.py
+++ b/jcvi/graphics/histogram.py
@@ -276,47 +276,47 @@ def main():
     """
     allowed_format = ("emf", "eps", "pdf", "png", "ps", "raw", "rgba", "svg", "svgz")
     p = OptionParser(main.__doc__)
-    p.add_option("--skip", default=0, type=int, help="skip the first several lines")
-    p.add_option("--col", default=0, type=int, help="Get the n-th column")
+    p.add_argument("--skip", default=0, type=int, help="skip the first several lines")
+    p.add_argument("--col", default=0, type=int, help="Get the n-th column")
     p.set_histogram()
-    p.add_option(
+    p.add_argument(
         "--tags",
         dest="tags",
         default=None,
         help="tags for data if multiple input files, comma sep",
     )
-    p.add_option(
+    p.add_argument(
         "--ascii",
         default=False,
         action="store_true",
         help="print ASCII text stem-leaf plot",
     )
-    p.add_option(
+    p.add_argument(
         "--base",
         default="0",
         choices=("0", "2", "10"),
         help="use logarithm axis with base, 0 to disable",
     )
-    p.add_option(
+    p.add_argument(
         "--facet",
         default=False,
         action="store_true",
         help="place multiple histograms side-by-side",
     )
-    p.add_option("--fill", default="white", help="color of the bin")
-    p.add_option(
+    p.add_argument("--fill", default="white", help="color of the bin")
+    p.add_argument(
         "--format",
         default="pdf",
         choices=allowed_format,
         help="Generate image of format",
     )
-    p.add_option(
+    p.add_argument(
         "--quick",
         default=False,
         action="store_true",
         help="Use quick plot, assuming bins are already counted",
     )
-    p.add_option(
+    p.add_argument(
         "--noprintstats",
         default=False,
         action="store_true",
diff --git a/jcvi/graphics/karyotype.py b/jcvi/graphics/karyotype.py
index a7957580..c1119000 100644
--- a/jcvi/graphics/karyotype.py
+++ b/jcvi/graphics/karyotype.py
@@ -403,31 +403,31 @@ def __init__(
 
 def main():
     p = OptionParser(__doc__)
-    p.add_option(
+    p.add_argument(
         "--basepair",
         default=False,
         action="store_true",
         help="Use base pair position instead of gene rank",
     )
-    p.add_option(
+    p.add_argument(
         "--keep-chrlabels",
         default=False,
         action="store_true",
         help="Keep chromosome labels",
     )
-    p.add_option(
+    p.add_argument(
         "--nocircles",
         default=False,
         action="store_true",
         help="Do not plot chromosome circles",
     )
-    p.add_option(
+    p.add_argument(
         "--shadestyle",
         default="curve",
         choices=Shade.Styles,
         help="Style of syntenic wedges",
     )
-    p.add_option(
+    p.add_argument(
         "--chrstyle",
         default="auto",
         choices=Chromosome.Styles,
diff --git a/jcvi/graphics/landscape.py b/jcvi/graphics/landscape.py
index 663e12cf..146c1034 100644
--- a/jcvi/graphics/landscape.py
+++ b/jcvi/graphics/landscape.py
@@ -205,8 +205,8 @@ def mosdepth(args):
     sns.set_style("darkgrid")
 
     p = OptionParser(mosdepth.__doc__)
-    p.add_option("--maxdepth", default=100, type=int, help="Maximum depth to plot")
-    p.add_option(
+    p.add_argument("--maxdepth", default=100, type=int, help="Maximum depth to plot")
+    p.add_argument(
         "--logscale", default=False, action="store_true", help="Use log-scale on depth"
     )
     opts, args, iopts = p.set_image_options(args, style="dark", figsize="6x8")
@@ -494,15 +494,15 @@ def depth(args):
     composite figure.
     """
     p = OptionParser(depth.__doc__)
-    p.add_option(
+    p.add_argument(
         "--chrinfo", help="Comma-separated mappings between seqid, color, new_name"
     )
-    p.add_option(
+    p.add_argument(
         "--titleinfo",
         help="Comma-separated titles mappings between filename, title",
     )
-    p.add_option("--maxdepth", default=100, type=int, help="Maximum depth to show")
-    p.add_option(
+    p.add_argument("--maxdepth", default=100, type=int, help="Maximum depth to show")
+    p.add_argument(
         "--logscale", default=False, action="store_true", help="Use log-scale on depth"
     )
     opts, args, iopts = p.set_image_options(args, style="dark", figsize="14x4")
@@ -548,10 +548,10 @@ def add_window_options(p):
     """
     Add options for window plotting.
     """
-    p.add_option("--window", default=500000, type=int, help="Size of window")
-    p.add_option("--shift", default=100000, type=int, help="Size of shift")
-    p.add_option("--subtract", help="Subtract bases from window")
-    p.add_option(
+    p.add_argument("--window", default=500000, type=int, help="Size of window")
+    p.add_argument("--shift", default=100000, type=int, help="Size of shift")
+    p.add_argument("--subtract", help="Subtract bases from window")
+    p.add_argument(
         "--nomerge", default=False, action="store_true", help="Do not merge features"
     )
 
@@ -641,16 +641,16 @@ def composite(args):
     --altbars: similar to bars, yet in two alternating tracks, e.g. scaffolds
     """
     p = OptionParser(composite.__doc__)
-    p.add_option("--lines", help="Features to plot in lineplot")
-    p.add_option("--bars", help="Features to plot in bars")
-    p.add_option("--altbars", help="Features to plot in alt-bars")
-    p.add_option(
+    p.add_argument("--lines", help="Features to plot in lineplot")
+    p.add_argument("--bars", help="Features to plot in bars")
+    p.add_argument("--altbars", help="Features to plot in alt-bars")
+    p.add_argument(
         "--fatten",
         default=False,
         action="store_true",
         help="Help visualize certain narrow features",
     )
-    p.add_option(
+    p.add_argument(
         "--mode",
         default="span",
         choices=("span", "count", "score"),
@@ -754,22 +754,22 @@ def multilineplot(args):
     --lines: traditional line plots, useful for plotting feature freq
     """
     p = OptionParser(multilineplot.__doc__)
-    p.add_option("--lines", help="Features to plot in lineplot")
-    p.add_option("--colors", help="List of colors matching number of input bed files")
-    p.add_option(
+    p.add_argument("--lines", help="Features to plot in lineplot")
+    p.add_argument("--colors", help="List of colors matching number of input bed files")
+    p.add_argument(
         "--mode",
         default="span",
         choices=("span", "count", "score"),
         help="Accumulate feature based on",
     )
-    p.add_option(
+    p.add_argument(
         "--binned",
         default=False,
         action="store_true",
         help="Specify whether the input is already binned; "
         + "if True, input files are considered to be binfiles",
     )
-    p.add_option("--ymax", type=int, help="Set Y-axis max")
+    p.add_argument("--ymax", type=int, help="Set Y-axis max")
     add_window_options(p)
     opts, args, iopts = p.set_image_options(args, figsize="8x5")
 
@@ -946,17 +946,17 @@ def heatmap(args):
     given chromosome. Need to give multiple beds to --stacks and --heatmaps
     """
     p = OptionParser(heatmap.__doc__)
-    p.add_option(
+    p.add_argument(
         "--stacks",
         default="Exons,Introns,DNA_transposons,Retrotransposons",
         help="Features to plot in stackplot",
     )
-    p.add_option(
+    p.add_argument(
         "--heatmaps",
         default="Copia,Gypsy,hAT,Helitron,Introns,Exons",
         help="Features to plot in heatmaps",
     )
-    p.add_option("--meres", default=None, help="Extra centromere / telomere features")
+    p.add_argument("--meres", default=None, help="Extra centromere / telomere features")
     add_window_options(p)
     opts, args, iopts = p.set_image_options(args, figsize="8x5")
 
@@ -1172,13 +1172,13 @@ def stack(args):
     sequences along the chromosomes.
     """
     p = OptionParser(stack.__doc__)
-    p.add_option("--top", default=10, type=int, help="Draw the first N chromosomes")
-    p.add_option(
+    p.add_argument("--top", default=10, type=int, help="Draw the first N chromosomes")
+    p.add_argument(
         "--stacks",
         default="Exons,Introns,DNA_transposons,Retrotransposons",
         help="Features to plot in stackplot",
     )
-    p.add_option("--switch", help="Change chr names based on two-column file")
+    p.add_argument("--switch", help="Change chr names based on two-column file")
     add_window_options(p)
     opts, args, iopts = p.set_image_options(args, figsize="8x8")
 
diff --git a/jcvi/graphics/mummerplot.py b/jcvi/graphics/mummerplot.py
index db513aef..ce11408a 100644
--- a/jcvi/graphics/mummerplot.py
+++ b/jcvi/graphics/mummerplot.py
@@ -32,26 +32,26 @@ def main(args):
     query. Control "major" by option --refcov.
     """
     p = OptionParser(main.__doc__)
-    p.add_option("--refids", help="Use subset of contigs in the ref")
-    p.add_option(
+    p.add_argument("--refids", help="Use subset of contigs in the ref")
+    p.add_argument(
         "--refcov",
         default=0.01,
         type=float,
         help="Minimum reference coverage",
     )
-    p.add_option(
+    p.add_argument(
         "--all",
         default=False,
         action="store_true",
         help="Plot one pdf file per ref in refidsfile",
     )
-    p.add_option(
+    p.add_argument(
         "--color",
         default="similarity",
         choices=("similarity", "direction", "none"),
         help="Color the dots based on",
     )
-    p.add_option(
+    p.add_argument(
         "--nolayout",
         default=False,
         action="store_true",
diff --git a/jcvi/graphics/synteny.py b/jcvi/graphics/synteny.py
index 7a170cd0..d69facea 100644
--- a/jcvi/graphics/synteny.py
+++ b/jcvi/graphics/synteny.py
@@ -628,14 +628,14 @@ def draw_gene_legend(
 
 def main():
     p = OptionParser(__doc__)
-    p.add_option("--switch", help="Rename the seqid with two-column file")
-    p.add_option("--tree", help="Display trees on the bottom of the figure")
-    p.add_option("--extra", help="Extra features in BED format")
-    p.add_option(
+    p.add_argument("--switch", help="Rename the seqid with two-column file")
+    p.add_argument("--tree", help="Display trees on the bottom of the figure")
+    p.add_argument("--extra", help="Extra features in BED format")
+    p.add_argument(
         "--genelabels",
         help='Show only these gene labels, separated by comma. Example: "At1g12340,At5g54690"',
     )
-    p.add_option(
+    p.add_argument(
         "--genelabelsize",
         default=0,
         type=int,
@@ -643,43 +643,43 @@ def main():
         + "However, plot may appear visually crowded. "
         + "Reasonably good values are 2 to 6 [Default: disabled]",
     )
-    p.add_option(
+    p.add_argument(
         "--genelabelrotation",
         default=25,
         type=int,
         help="Rotate gene labels at this angle (anti-clockwise), useful for debugging. "
         + "[Default: 25]",
     )
-    p.add_option(
+    p.add_argument(
         "--scalebar",
         default=False,
         action="store_true",
         help="Add scale bar to the plot",
     )
-    p.add_option(
+    p.add_argument(
         "--glyphstyle",
         default="box",
         choices=Glyph.Styles,
         help="Style of feature glyphs",
     )
-    p.add_option(
+    p.add_argument(
         "--glyphcolor",
         default="orientation",
         choices=Glyph.Palette,
         help="Glyph coloring based on",
     )
-    p.add_option(
+    p.add_argument(
         "--shadestyle",
         default="curve",
         choices=Shade.Styles,
         help="Style of syntenic wedges",
     )
-    p.add_option(
+    p.add_argument(
         "--outputprefix",
         default="",
         help="Prefix for the output file",
     )
-    p.add_option(
+    p.add_argument(
         "--noprune",
         default=False,
         action="store_true",
diff --git a/jcvi/graphics/tree.py b/jcvi/graphics/tree.py
index ff2d0408..a9daa222 100644
--- a/jcvi/graphics/tree.py
+++ b/jcvi/graphics/tree.py
@@ -548,44 +548,46 @@ def main(args):
     on, also show the number of amino acids.
     """
     p = OptionParser(main.__doc__)
-    p.add_option(
+    p.add_argument(
         "--outgroup",
         help="Outgroup for rerooting the tree. "
         + "Use comma to separate multiple taxa.",
     )
-    p.add_option(
+    p.add_argument(
         "--noreroot",
         default=False,
         action="store_true",
         help="Don't reroot the input tree",
     )
-    p.add_option(
+    p.add_argument(
         "--rmargin", default=0.2, type=float, help="Set blank rmargin to the right"
     )
-    p.add_option("--gffdir", default=None, help="The directory that contain GFF files")
-    p.add_option("--sizes", default=None, help="The FASTA file or the sizes file")
-    p.add_option("--SH", default=None, type=str, help="SH test p-value")
-
-    group = p.add_option_group("Node style")
-    group.add_option("--leafcolor", default="k", help="Font color for the OTUs")
-    group.add_option("--leaffont", default=12, help="Font size for the OTUs")
-    group.add_option(
+    p.add_argument(
+        "--gffdir", default=None, help="The directory that contain GFF files"
+    )
+    p.add_argument("--sizes", default=None, help="The FASTA file or the sizes file")
+    p.add_argument("--SH", default=None, type=str, help="SH test p-value")
+
+    group = p.add_argument_group("Node style")
+    group.add_argument("--leafcolor", default="k", help="Font color for the OTUs")
+    group.add_argument("--leaffont", default=12, help="Font size for the OTUs")
+    group.add_argument(
         "--leafinfo", help="CSV file specifying the leaves: name,color,new_name"
     )
-    group.add_option(
+    group.add_argument(
         "--scutoff",
         default=0,
         type=int,
         help="cutoff for displaying node support, 0-100",
     )
-    group.add_option(
+    group.add_argument(
         "--no_support",
         dest="support",
         default=True,
         action="store_false",
         help="Do not print node support values",
     )
-    group.add_option(
+    group.add_argument(
         "--no_internal",
         dest="internal",
         default=True,
@@ -593,25 +595,25 @@ def main(args):
         help="Do not show internal nodes",
     )
 
-    group = p.add_option_group("Edge style")
-    group.add_option(
+    group = p.add_argument_group("Edge style")
+    group.add_argument(
         "--dashedoutgroup",
         default=False,
         action="store_true",
         help="Gray out the edges connecting outgroup and non-outgroup",
     )
 
-    group = p.add_option_group("Additional annotations")
-    group.add_option(
+    group = p.add_argument_group("Additional annotations")
+    group.add_argument(
         "--geoscale",
         default=False,
         action="store_true",
         help="Plot geological scale",
     )
-    group.add_option(
+    group.add_argument(
         "--wgdinfo", help="CSV specifying the position and style of WGD events"
     )
-    group.add_option(
+    group.add_argument(
         "--groups",
         help="Group names from top to bottom, to the right of the tree. "
         "Each distinct color in --leafinfo is considered part of the same group. "
diff --git a/jcvi/graphics/wheel.py b/jcvi/graphics/wheel.py
index 86fc339f..1cdbb493 100644
--- a/jcvi/graphics/wheel.py
+++ b/jcvi/graphics/wheel.py
@@ -73,7 +73,7 @@ def wheel(args):
     Wheel plot that shows continous data in radial axes.
     """
     p = OptionParser(wheel.__doc__)
-    p.add_option(
+    p.add_argument(
         "--column",
         default="score",
         choices=("score", "percentile"),
diff --git a/jcvi/projects/ies.py b/jcvi/projects/ies.py
index 294bbbc5..c005039d 100644
--- a/jcvi/projects/ies.py
+++ b/jcvi/projects/ies.py
@@ -47,7 +47,7 @@ def variation(args):
     Associate IES in parents and progeny.
     """
     p = OptionParser(variation.__doc__)
-    p.add_option(
+    p.add_argument(
         "--diversity",
         choices=("breakpoint", "variant"),
         default="variant",
@@ -197,7 +197,7 @@ def insertionpairs(args):
             (RE)   (LE)
     """
     p = OptionParser(insertionpairs.__doc__)
-    p.add_option(
+    p.add_argument(
         "--extend",
         default=10,
         type=int,
@@ -240,7 +240,7 @@ def insertion(args):
     'lesions' (stack of broken reads) in the MAC genome.
     """
     p = OptionParser(insertion.__doc__)
-    p.add_option(
+    p.add_argument(
         "--mindepth", default=6, type=int, help="Minimum depth to call an insertion"
     )
     p.set_outfile()
@@ -276,13 +276,13 @@ def deletion(args):
     Find IES based on mapping MAC reads to MIC genome.
     """
     p = OptionParser(deletion.__doc__)
-    p.add_option(
+    p.add_argument(
         "--mindepth", default=3, type=int, help="Minimum depth to call a deletion"
     )
-    p.add_option(
+    p.add_argument(
         "--minspan", default=30, type=int, help="Minimum span to call a deletion"
     )
-    p.add_option(
+    p.add_argument(
         "--split",
         default=False,
         action="store_true",
diff --git a/jcvi/projects/misc.py b/jcvi/projects/misc.py
index 7c074ac3..1c739611 100644
--- a/jcvi/projects/misc.py
+++ b/jcvi/projects/misc.py
@@ -180,7 +180,7 @@ def utricularia(args):
     from jcvi.graphics.synteny import main as synteny_main
 
     p = OptionParser(synteny_main.__doc__)
-    p.add_option("--switch", help="Rename the seqid with two-column file")
+    p.add_argument("--switch", help="Rename the seqid with two-column file")
     opts, args, iopts = p.set_image_options(args, figsize="8x7")
 
     if len(args) != 3:
@@ -377,7 +377,7 @@ def oropetium(args):
     Build a composite figure that calls graphis.synteny.
     """
     p = OptionParser(oropetium.__doc__)
-    p.add_option("--extra", help="Extra features in BED format")
+    p.add_argument("--extra", help="Extra features in BED format")
     opts, args, iopts = p.set_image_options(args, figsize="9x6")
 
     if len(args) != 4:
@@ -493,8 +493,8 @@ def amborella(args):
     Build a composite figure that calls graphics.karyotype and graphics.synteny.
     """
     p = OptionParser(amborella.__doc__)
-    p.add_option("--tree", help="Display trees on the bottom of the figure")
-    p.add_option("--switch", help="Rename the seqid with two-column file")
+    p.add_argument("--tree", help="Display trees on the bottom of the figure")
+    p.add_argument("--switch", help="Rename the seqid with two-column file")
     opts, args, iopts = p.set_image_options(args, figsize="8x7")
 
     if len(args) != 5:
@@ -540,8 +540,8 @@ def cotton(args):
     Build a composite figure that calls graphics.karyotype and graphic.synteny.
     """
     p = OptionParser(cotton.__doc__)
-    p.add_option("--depthfile", help="Use depth info in this file")
-    p.add_option("--switch", help="Rename the seqid with two-column file")
+    p.add_argument("--depthfile", help="Use depth info in this file")
+    p.add_argument("--switch", help="Rename the seqid with two-column file")
     opts, args, iopts = p.set_image_options(args, figsize="8x7")
 
     if len(args) != 5:
diff --git a/jcvi/projects/napus.py b/jcvi/projects/napus.py
index 454d163f..69c8c009 100644
--- a/jcvi/projects/napus.py
+++ b/jcvi/projects/napus.py
@@ -129,21 +129,21 @@ def cov(args):
     homeologous gene pairs. Allow multiple chromosomes to multiple chromosomes.
     """
     p = OptionParser(cov.__doc__)
-    p.add_option(
+    p.add_argument(
         "--order",
         default="swede,kale,h165,yudal,aviso,abu,bristol,bzh",
         help="The order to plot the tracks, comma-separated",
     )
-    p.add_option(
+    p.add_argument(
         "--reverse",
         default=False,
         action="store_true",
         help="Plot the order in reverse",
     )
-    p.add_option(
+    p.add_argument(
         "--gauge_step", default=5000000, type=int, help="Step size for the base scale"
     )
-    p.add_option(
+    p.add_argument(
         "--hlsuffix",
         default="regions.forhaibao",
         help="Suffix for the filename to be used to highlight regions",
@@ -284,7 +284,7 @@ def fig3(args):
     from jcvi.formats.bed import Bed
 
     p = OptionParser(fig3.__doc__)
-    p.add_option(
+    p.add_argument(
         "--gauge_step",
         default=10000000,
         type=int,
@@ -533,7 +533,7 @@ def fig4(args):
     showing read alignments from high GL and low GL lines.
     """
     p = OptionParser(fig4.__doc__)
-    p.add_option(
+    p.add_argument(
         "--gauge_step", default=200000, type=int, help="Step size for the base scale"
     )
     opts, args, iopts = p.set_image_options(args, figsize="9x7")
diff --git a/jcvi/projects/pineapple.py b/jcvi/projects/pineapple.py
index 7aa522ac..8be49b63 100644
--- a/jcvi/projects/pineapple.py
+++ b/jcvi/projects/pineapple.py
@@ -71,7 +71,7 @@ def flanking(args):
     Extract flanking genes for given SI loci.
     """
     p = OptionParser(flanking.__doc__)
-    p.add_option("-N", default=50, type=int, help="How many genes on both directions")
+    p.add_argument("-N", default=50, type=int, help="How many genes on both directions")
     opts, args = p.parse_args(args)
 
     if len(args) != 4:
@@ -300,7 +300,7 @@ def ploidy(args):
     and graphic.synteny.
     """
     p = OptionParser(ploidy.__doc__)
-    p.add_option("--switch", help="Rename the seqid with two-column file")
+    p.add_argument("--switch", help="Rename the seqid with two-column file")
     opts, args, iopts = p.set_image_options(args, figsize="9x7")
 
     if len(args) != 5:
diff --git a/jcvi/projects/str.py b/jcvi/projects/str.py
index 538e9099..9ffac1b6 100644
--- a/jcvi/projects/str.py
+++ b/jcvi/projects/str.py
@@ -283,7 +283,7 @@ def mendelian2(args):
     counts and gender information to correct error estimate of X-linked loci.
     """
     p = OptionParser(mendelian2.__doc__)
-    p.add_option(
+    p.add_argument(
         "--treds", default=None, help="Extract specific treds, use comma to separate"
     )
     opts, args = p.parse_args(args)
@@ -764,7 +764,7 @@ def mendelian(args):
     Calculate Mendelian errors based on trios and duos.
     """
     p = OptionParser(mendelian.__doc__)
-    p.add_option("--tolerance", default=0, type=int, help="Tolernace for differences")
+    p.add_argument("--tolerance", default=0, type=int, help="Tolernace for differences")
     p.set_verbose()
     opts, args = p.parse_args(args)
 
@@ -884,10 +884,10 @@ def mini(args):
     Prepare mini-BAMs that contain only the STR loci.
     """
     p = OptionParser(mini.__doc__)
-    p.add_option(
+    p.add_argument(
         "--pad", default=20000, type=int, help="Add padding to the STR reigons"
     )
-    p.add_option(
+    p.add_argument(
         "--treds", default=None, help="Extract specific treds, use comma to separate"
     )
     p.set_outfile()
@@ -1439,13 +1439,13 @@ def allelefreq(args):
     Plot the allele frequencies of some STRs.
     """
     p = OptionParser(allelefreq.__doc__)
-    p.add_option(
+    p.add_argument(
         "--nopanels",
         default=False,
         action="store_true",
         help="No panel labels A, B, ...",
     )
-    p.add_option("--usereport", help="Use allele frequency in report file")
+    p.add_argument("--usereport", help="Use allele frequency in report file")
     opts, args, iopts = p.set_image_options(args, figsize="9x13")
 
     if len(args) != 1:
@@ -1500,8 +1500,8 @@ def make_fasta(seq, fastafile, id):
 
 
 def add_simulate_options(p):
-    p.add_option("--readlen", default=150, type=int, help="Length of the read")
-    p.add_option(
+    p.add_argument("--readlen", default=150, type=int, help="Length of the read")
+    p.add_argument(
         "--distance",
         default=500,
         type=int,
@@ -1519,16 +1519,16 @@ def simulate(args):
     `run_dir`.
     """
     p = OptionParser(simulate.__doc__)
-    p.add_option(
+    p.add_argument(
         "--method", choices=("wgsim", "eagle"), default="eagle", help="Read simulator"
     )
-    p.add_option(
+    p.add_argument(
         "--ref",
         default="hg38",
         choices=("hg38", "hg19"),
         help="Reference genome version",
     )
-    p.add_option("--tred", default="HD", help="TRED locus")
+    p.add_argument("--tred", default="HD", help="TRED locus")
     add_simulate_options(p)
     opts, args = p.parse_args(args)
 
@@ -1642,7 +1642,7 @@ def batchlobstr(args):
     $ tred.py bamlist --haploid chr4 --workdir tredparse_results
     """
     p = OptionParser(batchlobstr.__doc__)
-    p.add_option(
+    p.add_argument(
         "--haploid", default="chrY,chrM", help="Use haploid model for these chromosomes"
     )
     p.set_cpus()
@@ -1703,7 +1703,7 @@ def evidences(args):
     - Longer allele
     """
     p = OptionParser(evidences.__doc__)
-    p.add_option(
+    p.add_argument(
         "--csv", default="hli.20170328.tred.tsv", help="TRED csv output to plot"
     )
     opts, args, iopts = p.set_image_options(args, format="pdf")
@@ -2044,7 +2044,9 @@ def compare2(args):
     Compare performances of various variant callers on simulated STR datasets.
     """
     p = OptionParser(compare2.__doc__)
-    p.add_option("--maxinsert", default=300, type=int, help="Maximum number of repeats")
+    p.add_argument(
+        "--maxinsert", default=300, type=int, help="Maximum number of repeats"
+    )
     add_simulate_options(p)
     opts, args, iopts = p.set_image_options(args, figsize="10x5")
 
@@ -2099,7 +2101,9 @@ def power(args):
     This compares the power of various evidence types.
     """
     p = OptionParser(power.__doc__)
-    p.add_option("--maxinsert", default=300, type=int, help="Maximum number of repeats")
+    p.add_argument(
+        "--maxinsert", default=300, type=int, help="Maximum number of repeats"
+    )
     add_simulate_options(p)
     opts, args, iopts = p.set_image_options(args, figsize="10x10", format="png")
 
@@ -2196,7 +2200,9 @@ def tredparse(args):
     Adds coverage comparisons as panel C and D.
     """
     p = OptionParser(tredparse.__doc__)
-    p.add_option("--maxinsert", default=300, type=int, help="Maximum number of repeats")
+    p.add_argument(
+        "--maxinsert", default=300, type=int, help="Maximum number of repeats"
+    )
     add_simulate_options(p)
     opts, args, iopts = p.set_image_options(args, figsize="10x10")
 
diff --git a/jcvi/projects/sugarcane.py b/jcvi/projects/sugarcane.py
index 3c91acf4..0e4767f5 100644
--- a/jcvi/projects/sugarcane.py
+++ b/jcvi/projects/sugarcane.py
@@ -418,13 +418,13 @@ def simulate(args):
     sns.set_style("darkgrid")
 
     p = OptionParser(simulate.__doc__)
-    p.add_option(
+    p.add_argument(
         "--verbose",
         default=False,
         action="store_true",
         help="Verbose logging during simulation",
     )
-    p.add_option("-N", default=10000, type=int, help="Number of simulated samples")
+    p.add_argument("-N", default=10000, type=int, help="Number of simulated samples")
     opts, args, iopts = p.set_image_options(args, figsize="6x6")
     if len(args) != 1:
         sys.exit(not p.print_help())
@@ -669,8 +669,8 @@ def divergence(args):
     sns.set_style("white")
 
     p = OptionParser(divergence.__doc__)
-    p.add_option("--title", default="Gapless", help="Plot title")
-    p.add_option(
+    p.add_argument("--title", default="Gapless", help="Plot title")
+    p.add_argument(
         "--xmin",
         default=94,
         type=int,
diff --git a/jcvi/projects/tgbs.py b/jcvi/projects/tgbs.py
index 8163f956..f1bc9f4b 100644
--- a/jcvi/projects/tgbs.py
+++ b/jcvi/projects/tgbs.py
@@ -164,12 +164,12 @@ def mstmap(args):
     from jcvi.assembly.geneticmap import MSTMatrix
 
     p = OptionParser(mstmap.__doc__)
-    p.add_option(
+    p.add_argument(
         "--population_type",
         default="RIL6",
         help="Type of population, possible values are DH and RILd",
     )
-    p.add_option(
+    p.add_argument(
         "--missing_threshold",
         default=0.5,
         help="Missing threshold, .25 excludes any marker with >25% missing",
@@ -207,8 +207,8 @@ def weblogo(args):
     from rich.progress import Progress
 
     p = OptionParser(weblogo.__doc__)
-    p.add_option("-N", default=10, type=int, help="Count the first and last N bases")
-    p.add_option("--nreads", default=1000000, type=int, help="Parse first N reads")
+    p.add_argument("-N", default=10, type=int, help="Count the first and last N bases")
+    p.add_argument("--nreads", default=1000000, type=int, help="Parse first N reads")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -286,7 +286,7 @@ def count(args):
     from jcvi.utils.cbook import SummaryStats
 
     p = OptionParser(count.__doc__)
-    p.add_option("--csv", help="Write depth per contig to file")
+    p.add_argument("--csv", help="Write depth per contig to file")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -335,7 +335,7 @@ def novo(args):
     from jcvi.apps.cdhit import filter as cdhit_filter
 
     p = OptionParser(novo.__doc__)
-    p.add_option(
+    p.add_argument(
         "--technology",
         choices=("illumina", "454", "iontorrent"),
         default="iontorrent",
diff --git a/jcvi/utils/aws.py b/jcvi/utils/aws.py
index e5b080cc..3d738616 100644
--- a/jcvi/utils/aws.py
+++ b/jcvi/utils/aws.py
@@ -144,14 +144,14 @@ def start(args):
     Launch ec2 instance through command line.
     """
     p = OptionParser(start.__doc__)
-    p.add_option(
+    p.add_argument(
         "--ondemand",
         default=False,
         action="store_true",
         help="Do we want a more expensive on-demand instance",
     )
-    p.add_option("--profile", default="mvrad-datasci-role", help="Profile name")
-    p.add_option("--price", default=4.0, type=float, help="Spot price")
+    p.add_argument("--profile", default="mvrad-datasci-role", help="Profile name")
+    p.add_argument("--price", default=4.0, type=float, help="Spot price")
     opts, args = p.parse_args(args)
 
     if len(args) != 0:
@@ -257,7 +257,7 @@ def stop(args):
     Stop EC2 instance.
     """
     p = OptionParser(stop.__doc__)
-    p.add_option("--profile", default="mvrad-datasci-role", help="Profile name")
+    p.add_argument("--profile", default="mvrad-datasci-role", help="Profile name")
     opts, args = p.parse_args(args)
 
     if len(args) != 0:
@@ -362,7 +362,7 @@ def cp(args):
     Copy files to folder. Accepts list of s3 addresses as input.
     """
     p = OptionParser(cp.__doc__)
-    p.add_option(
+    p.add_argument(
         "--force", default=False, action="store_true", help="Force overwrite if exists"
     )
     p.set_cpus()
@@ -405,8 +405,8 @@ def ls(args):
     List files with support for wildcards.
     """
     p = OptionParser(ls.__doc__)
-    p.add_option("--keys", help="List of keys to include")
-    p.add_option(
+    p.add_argument("--keys", help="List of keys to include")
+    p.add_argument(
         "--recursive", default=False, action="store_true", help="Recursive search"
     )
     opts, args = p.parse_args(args)
@@ -510,8 +510,8 @@ def role(args):
     ) = "205134639408 htang 114692162163 mvrad-datasci-role".split()
 
     p = OptionParser(role.__doc__)
-    p.add_option("--profile", default="mvrad-datasci-role", help="Profile name")
-    p.add_option(
+    p.add_argument("--profile", default="mvrad-datasci-role", help="Profile name")
+    p.add_argument(
         "--device",
         default="arn:aws:iam::" + src_acct + ":mfa/" + src_username,
         metavar="arn:aws:iam::123456788990:mfa/dudeman",
@@ -519,7 +519,7 @@ def role(args):
         "provided via the environment variable 'MFA_DEVICE' or"
         " the ~/.aws/credentials variable 'aws_mfa_device'.",
     )
-    p.add_option(
+    p.add_argument(
         "--duration",
         type=int,
         default=3600,
@@ -531,7 +531,7 @@ def role(args):
         "can also be provided via the environment "
         "variable 'MFA_STS_DURATION'. ",
     )
-    p.add_option(
+    p.add_argument(
         "--assume-role",
         "--assume",
         default="arn:aws:iam::" + dst_acct + ":role/" + dst_role,
@@ -540,12 +540,12 @@ def role(args):
         "assume, if specified. This value can also be provided"
         " via the environment variable 'MFA_ASSUME_ROLE'",
     )
-    p.add_option(
+    p.add_argument(
         "--role-session-name",
         help="Friendly session name required when using --assume-role",
         default=getpass.getuser(),
     )
-    p.add_option(
+    p.add_argument(
         "--force",
         help="Refresh credentials even if currently valid.",
         action="store_true",
diff --git a/jcvi/utils/db.py b/jcvi/utils/db.py
index 05a527dd..043abb49 100644
--- a/jcvi/utils/db.py
+++ b/jcvi/utils/db.py
@@ -171,7 +171,7 @@ def pull(args):
     """
     p = OptionParser(pull.__doc__)
     p.set_db_opts(dbname="mtg2", credentials=None)
-    p.add_option(
+    p.add_argument(
         "--frag",
         default=False,
         action="store_true",
@@ -239,7 +239,7 @@ def query(args):
     """
     p = OptionParser(query.__doc__)
     p.set_db_opts()
-    p.add_option(
+    p.add_argument(
         "--dryrun",
         default=False,
         action="store_true",
diff --git a/jcvi/variation/cnv.py b/jcvi/variation/cnv.py
index 8e35aa62..00e0056d 100644
--- a/jcvi/variation/cnv.py
+++ b/jcvi/variation/cnv.py
@@ -804,7 +804,7 @@ def cib(args):
     Convert BAM to CIB (a binary storage of int8 per base).
     """
     p = OptionParser(cib.__doc__)
-    p.add_option("--prefix", help="Report seqids with this prefix only")
+    p.add_argument("--prefix", help="Report seqids with this prefix only")
     p.set_cpus()
     opts, args = p.parse_args(args)
 
@@ -837,7 +837,7 @@ def batchcn(args):
     Run CNV segmentation caller in batch mode. Scans a workdir.
     """
     p = OptionParser(batchcn.__doc__)
-    p.add_option(
+    p.add_argument(
         "--upload",
         default="s3://hli-mv-data-science/htang/ccn",
         help="Upload cn and seg results to s3",
@@ -878,14 +878,14 @@ def hmm(args):
     directory.
     """
     p = OptionParser(hmm.__doc__)
-    p.add_option("--mu", default=0.003, type=float, help="Transition probability")
-    p.add_option(
+    p.add_argument("--mu", default=0.003, type=float, help="Transition probability")
+    p.add_argument(
         "--sigma",
         default=0.1,
         type=float,
         help="Standard deviation of Gaussian emission distribution",
     )
-    p.add_option(
+    p.add_argument(
         "--threshold",
         default=1,
         type=float,
@@ -1064,27 +1064,29 @@ def cn(args):
     Download CCN output folder and convert cib to copy number per 1Kb.
     """
     p = OptionParser(cn.__doc__)
-    p.add_option(
+    p.add_argument(
         "--binsize", default=1000, type=int, help="Window size along chromosome"
     )
-    p.add_option(
+    p.add_argument(
         "--cleanup",
         default=False,
         action="store_true",
         help="Clean up downloaded s3 folder",
     )
-    p.add_option(
+    p.add_argument(
         "--hmm",
         default=False,
         action="store_true",
         help="Run HMM caller after computing CN",
     )
-    p.add_option(
+    p.add_argument(
         "--upload",
         default="s3://hli-mv-data-science/htang/ccn",
         help="Upload cn and seg results to s3",
     )
-    p.add_option("--rebuildgc", help="Rebuild GC directory rather than pulling from S3")
+    p.add_argument(
+        "--rebuildgc", help="Rebuild GC directory rather than pulling from S3"
+    )
     opts, args = p.parse_args(args)
 
     if len(args) == 2:
@@ -1182,7 +1184,7 @@ def validate(args):
     Plot RDR/BAF/CN for validation of CNV calls in `sample.vcf.gz`.
     """
     p = OptionParser(validate.__doc__)
-    p.add_option(
+    p.add_argument(
         "--no-rdr-logy",
         default=False,
         action="store_true",
@@ -1421,7 +1423,7 @@ def wes_vs_wgs(args):
     Compare WES and WGS CNVs.
     """
     p = OptionParser(wes_vs_wgs.__doc__)
-    p.add_option(
+    p.add_argument(
         "--no-rdr-logy",
         default=False,
         action="store_true",
diff --git a/jcvi/variation/deconvolute.py b/jcvi/variation/deconvolute.py
index 30e788ae..df8f7409 100644
--- a/jcvi/variation/deconvolute.py
+++ b/jcvi/variation/deconvolute.py
@@ -141,19 +141,19 @@ def split(args):
     """
     p = OptionParser(split.__doc__)
     p.set_outdir(outdir="deconv")
-    p.add_option(
+    p.add_argument(
         "--nocheckprefix",
         default=False,
         action="store_true",
         help="Don't check shared prefix",
     )
-    p.add_option(
+    p.add_argument(
         "--paired",
         default=False,
         action="store_true",
         help="Paired-end data",
     )
-    p.add_option(
+    p.add_argument(
         "--append",
         default=False,
         action="store_true",
diff --git a/jcvi/variation/delly.py b/jcvi/variation/delly.py
index a07102f3..88c4ae15 100644
--- a/jcvi/variation/delly.py
+++ b/jcvi/variation/delly.py
@@ -86,8 +86,8 @@ def mitosomatic(args):
     import pandas as pd
 
     p = OptionParser(mitosomatic.__doc__)
-    p.add_option("--minaf", default=0.005, type=float, help="Minimum allele fraction")
-    p.add_option("--maxaf", default=0.1, type=float, help="Maximum allele fraction")
+    p.add_argument("--minaf", default=0.005, type=float, help="Minimum allele fraction")
+    p.add_argument("--maxaf", default=0.1, type=float, help="Maximum allele fraction")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -196,16 +196,16 @@ def mito(args):
     """
     p = OptionParser(mito.__doc__)
     p.set_aws_opts(store="hli-mv-data-science/htang/mito-deletions")
-    p.add_option(
+    p.add_argument(
         "--realignonly", default=False, action="store_true", help="Realign only"
     )
-    p.add_option(
+    p.add_argument(
         "--svonly",
         default=False,
         action="store_true",
         help="Run Realign => SV calls only",
     )
-    p.add_option(
+    p.add_argument(
         "--support", default=1, type=int, help="Minimum number of supporting reads"
     )
     p.set_home("speedseq", default="/mnt/software/speedseq/bin")
diff --git a/jcvi/variation/phase.py b/jcvi/variation/phase.py
index fe0530a7..8ce1a043 100644
--- a/jcvi/variation/phase.py
+++ b/jcvi/variation/phase.py
@@ -83,7 +83,7 @@ def prepare(args):
     - variants_to_phase: in format of phased vcf
     """
     p = OptionParser(prepare.__doc__)
-    p.add_option("--accuracy", default=0.85, help="Sequencing per-base accuracy")
+    p.add_argument("--accuracy", default=0.85, help="Sequencing per-base accuracy")
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
diff --git a/jcvi/variation/snp.py b/jcvi/variation/snp.py
index d8f65e02..d316326e 100644
--- a/jcvi/variation/snp.py
+++ b/jcvi/variation/snp.py
@@ -38,7 +38,7 @@ def mappability(args):
     <https://github.com/xuefzhao/Reference.Mappability>
     """
     p = OptionParser(mappability.__doc__)
-    p.add_option("--mer", default=50, type=int, help="User mer size")
+    p.add_argument("--mer", default=50, type=int, help="User mer size")
     p.set_cpus()
     opts, args = p.parse_args(args)
 
@@ -85,7 +85,7 @@ def gatk(args):
     Call SNPs based on GATK best practices.
     """
     p = OptionParser(gatk.__doc__)
-    p.add_option(
+    p.add_argument(
         "--indelrealign",
         default=False,
         action="store_true",
@@ -207,7 +207,7 @@ def rmdup(args):
     Remove PCR duplicates from BAM files, generate a list of commands.
     """
     p = OptionParser(rmdup.__doc__)
-    p.add_option(
+    p.add_argument(
         "-S", default=False, action="store_true", help="Treat PE reads as SE in rmdup"
     )
     opts, args = p.parse_args(args)
@@ -258,8 +258,8 @@ def freebayes(args):
     Call SNPs using freebayes.
     """
     p = OptionParser(freebayes.__doc__)
-    p.add_option("--mindepth", default=3, type=int, help="Minimum depth")
-    p.add_option("--minqual", default=20, type=int, help="Minimum quality")
+    p.add_argument("--mindepth", default=3, type=int, help="Minimum depth")
+    p.add_argument("--minqual", default=20, type=int, help="Minimum quality")
     opts, args = p.parse_args(args)
 
     if len(args) < 2:
@@ -283,8 +283,8 @@ def freq(args):
     Call SNP frequencies and generate GFF file.
     """
     p = OptionParser(freq.__doc__)
-    p.add_option("--mindepth", default=3, type=int, help="Minimum depth")
-    p.add_option("--minqual", default=20, type=int, help="Minimum quality")
+    p.add_argument("--mindepth", default=3, type=int, help="Minimum depth")
+    p.add_argument("--minqual", default=20, type=int, help="Minimum quality")
     p.set_outfile()
     opts, args = p.parse_args(args)
 
@@ -306,7 +306,7 @@ def frommaf(args):
     Convert to four-column tabular format from MAF.
     """
     p = OptionParser(frommaf.__doc__)
-    p.add_option("--validate", help="Validate coordinates against FASTA")
+    p.add_argument("--validate", help="Validate coordinates against FASTA")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
diff --git a/jcvi/variation/str.py b/jcvi/variation/str.py
index 51e7401f..072e4b65 100644
--- a/jcvi/variation/str.py
+++ b/jcvi/variation/str.py
@@ -390,7 +390,7 @@ def treds(args):
     from jcvi.apps.base import datafile
 
     p = OptionParser(treds.__doc__)
-    p.add_option(
+    p.add_argument(
         "--csv", default=False, action="store_true", help="Also write `meta.csv`"
     )
     opts, args = p.parse_args(args)
@@ -615,7 +615,7 @@ def meta(args):
     $ intersectBed -a all-STR.bed -b all-exons.bed -wo > STR-exons.wo.bed
     """
     p = OptionParser(meta.__doc__)
-    p.add_option(
+    p.add_argument(
         "--cutoff",
         default=0.5,
         type=float,
@@ -693,7 +693,7 @@ def bin(args):
     Conver tsv to binary format.
     """
     p = OptionParser(bin.__doc__)
-    p.add_option("--dtype", choices=("float32", "int32"), help="dtype of the matrix")
+    p.add_argument("--dtype", choices=("float32", "int32"), help="dtype of the matrix")
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -790,7 +790,7 @@ def data(args):
     Make data.tsv based on meta.tsv.
     """
     p = OptionParser(data.__doc__)
-    p.add_option(
+    p.add_argument(
         "--notsv", default=False, action="store_true", help="Do not write data.tsv"
     )
     opts, args = p.parse_args(args)
@@ -990,8 +990,8 @@ def compilevcf(args):
     Compile vcf results into master spreadsheet.
     """
     p = OptionParser(compilevcf.__doc__)
-    p.add_option("--db", default="hg38", help="Use these lobSTR db")
-    p.add_option(
+    p.add_argument("--db", default="hg38", help="Use these lobSTR db")
+    p.add_argument(
         "--nofilter",
         default=False,
         action="store_true",
@@ -1150,7 +1150,7 @@ def liftover(args):
     LiftOver CODIS/Y-STR markers.
     """
     p = OptionParser(liftover.__doc__)
-    p.add_option(
+    p.add_argument(
         "--checkvalid",
         default=False,
         action="store_true",
@@ -1192,24 +1192,24 @@ def trf(args):
     cparams = "1 1 2 80 5 200 2000"
 
     p = OptionParser(trf.__doc__)
-    p.add_option("--mismatch", default=31, type=int, help="Mismatch and gap penalty")
-    p.add_option(
+    p.add_argument("--mismatch", default=31, type=int, help="Mismatch and gap penalty")
+    p.add_argument(
         "--minscore", default=MINSCORE, type=int, help="Minimum score to report"
     )
-    p.add_option("--period", default=6, type=int, help="Maximum period to report")
-    p.add_option(
+    p.add_argument("--period", default=6, type=int, help="Maximum period to report")
+    p.add_argument(
         "--lobstr",
         default=False,
         action="store_true",
         help="Generate output for lobSTR",
     )
-    p.add_option(
+    p.add_argument(
         "--telomeres",
         default=False,
         action="store_true",
         help="Run telomere search: minscore=140 period=7",
     )
-    p.add_option(
+    p.add_argument(
         "--centromeres",
         default=False,
         action="store_true",
@@ -1267,7 +1267,7 @@ def batchlobstr(args):
     sample-name,s3-location
     """
     p = OptionParser(batchlobstr.__doc__)
-    p.add_option("--sep", default=",", help="Separator for building commandline")
+    p.add_argument("--sep", default=",", help="Separator for building commandline")
     p.set_home("lobstr", default="s3://hli-mv-data-science/htang/str-build/lobSTR/")
     p.set_aws_opts(store="hli-mv-data-science/htang/str-data")
     opts, args = p.parse_args(args)
@@ -1324,11 +1324,11 @@ def lobstr(args):
     (e.g. s3://hli-mv-data-science/htang/str-build/lobSTR/)
     """
     p = OptionParser(lobstr.__doc__)
-    p.add_option(
+    p.add_argument(
         "--haploid", default="chrY,chrM", help="Use haploid model for these chromosomes"
     )
-    p.add_option("--chr", help="Run only this chromosome")
-    p.add_option(
+    p.add_argument("--chr", help="Run only this chromosome")
+    p.add_argument(
         "--simulation", default=False, action="store_true", help="Simulation mode"
     )
     p.set_home("lobstr", default="s3://hli-mv-data-science/htang/str-build/lobSTR/")
@@ -1458,8 +1458,8 @@ def locus(args):
     db_choices = ("hg38", "hg19")
 
     p = OptionParser(locus.__doc__)
-    p.add_option("--tred", choices=INCLUDE, help="TRED name")
-    p.add_option("--ref", choices=db_choices, default="hg38", help="Reference genome")
+    p.add_argument("--tred", choices=INCLUDE, help="TRED name")
+    p.add_argument("--ref", choices=db_choices, default="hg38", help="Reference genome")
     p.set_home("lobstr")
     opts, args = p.parse_args(args)
 
@@ -1511,7 +1511,7 @@ def lobstrindex(args):
     by str().
     """
     p = OptionParser(lobstrindex.__doc__)
-    p.add_option(
+    p.add_argument(
         "--notreds",
         default=False,
         action="store_true",