Add ntedit

bio.txt

@@ -379,6 +379,7 @@ nhmmscan
 normalize-by-median.py
 normalize-iHS
 nquire
+ntedit
 nucmer
 nullarbor.pl
 octopus

bio/json/ntedit.json

@@ -0,0 +1 @@
+{"name":"ntedit","description":"Fast, lightweight, scalable genome sequence polishing and SNV detection & annotation","usage":"","options":[{"names":["-t"],"argument":"NUM","description":"number of threads [default=1]"},{"names":["-f"],"argument":"FILE","description":"draft genome assembly (FASTA, Multi-FASTA, and/or gzipped compatible), REQUIRED"},{"names":["-r"],"argument":"FILE","description":"Bloom filter file (generated from ntHits), REQUIRED"},{"names":["-e"],"argument":"FILE","description":"secondary Bloom filter with k-mers to reject (generated from ntHits), OPTIONAL"},{"names":["-b"],"argument":"STR","description":"output file prefix, OPTIONAL"},{"names":["-z"],"argument":"NUM","description":"minimum contig length [default=100]"},{"names":["-i"],"argument":"NUM","description":"maximum number of insertion bases to try, range 0-5, [default=5]"},{"names":["-d"],"argument":"NUM","description":"maximum number of deletions bases to try, range 0-10, [default=5]"},{"names":["-x"],"argument":"NUM","description":"k/x ratio for the number of k-mers that should be missing, [default=5.000]"},{"names":["-y"],"argument":"NUM","description":"k/y ratio for the number of edited k-mers that should be present, [default=9.000]"},{"names":["-X"],"argument":"NUM","description":"ratio of number of k-mers in the k subset that should be missing in order to attempt fix (higher=stringent), [default=0.5]"},{"names":["-Y"],"argument":"NUM","description":"ratio of number of k-mers in the k subset that should be present to accept an edit (higher=stringent), [default=0.5]"},{"names":["-c"],"argument":"NUM","description":"cap for the number of base insertions that can be made at one position, [default=k*1.5]"},{"names":["-j"],"argument":"NUM","description":"controls size of k-mer subset. When checking subset of k-mers, check every jth k-mer, [default=3]"},{"names":["-m"],"argument":"{0,1,2}","description":"mode of editing, range 0-2, [default=0] 0: best substitution, or first good indel 1: best substitution, or best indel 2: best edit overall (suggestion that you reduce i and d for performance)"},{"names":["-s"],"argument":"{0,1}","description":"SNV mode. Overrides draft k-mer checks, forcing reassessment at each position (-s 1 = yes, default = 0, no)"},{"names":["-l"],"argument":"FILE","description":"input VCF file with annotated variants (e.g., clinvar.vcf), OPTIONAL"},{"names":["-a"],"argument":"{0,1}","description":"soft masks missing k-mer positions having no fix (-v 1 = yes, default = 0, no)"},{"names":["-v"],"argument":"{0,1}","description":"verbose mode (-v 1 = yes, default = 0, no)"},{"names":["--help"],"argument":"","description":"display this message and exit"},{"names":["--version"],"argument":"","description":"output version information and exit"}],"version":"ntEdit v1.4.3"}

bio/yaml/ntedit.yaml

@@ -0,0 +1,89 @@
+name: ntedit
+description: Fast, lightweight, scalable genome sequence polishing and SNV detection & annotation
+usage: ""
+options:
+  - names:
+      - -t
+    argument: NUM
+    description: number of threads [default=1]
+  - names:
+      - -f
+    argument: FILE
+    description: draft genome assembly (FASTA, Multi-FASTA, and/or gzipped compatible), REQUIRED
+  - names:
+      - -r
+    argument: FILE
+    description: Bloom filter file (generated from ntHits), REQUIRED
+  - names:
+      - -e
+    argument: FILE
+    description: secondary Bloom filter with k-mers to reject (generated from ntHits), OPTIONAL
+  - names:
+      - -b
+    argument: STR
+    description: output file prefix, OPTIONAL
+  - names:
+      - -z
+    argument: NUM
+    description: minimum contig length [default=100]
+  - names:
+      - -i
+    argument: NUM
+    description: maximum number of insertion bases to try, range 0-5, [default=5]
+  - names:
+      - -d
+    argument: NUM
+    description: maximum number of deletions bases to try, range 0-10, [default=5]
+  - names:
+      - -x
+    argument: NUM
+    description: k/x ratio for the number of k-mers that should be missing, [default=5.000]
+  - names:
+      - -y
+    argument: NUM
+    description: k/y ratio for the number of edited k-mers that should be present, [default=9.000]
+  - names:
+      - -X
+    argument: NUM
+    description: ratio of number of k-mers in the k subset that should be missing in order to attempt fix (higher=stringent), [default=0.5]
+  - names:
+      - -Y
+    argument: NUM
+    description: ratio of number of k-mers in the k subset that should be present to accept an edit (higher=stringent), [default=0.5]
+  - names:
+      - -c
+    argument: NUM
+    description: cap for the number of base insertions that can be made at one position, [default=k*1.5]
+  - names:
+      - -j
+    argument: NUM
+    description: controls size of k-mer subset. When checking subset of k-mers, check every jth k-mer, [default=3]
+  - names:
+      - -m
+    argument: '{0,1,2}'
+    description: 'mode of editing, range 0-2, [default=0] 0: best substitution, or first good indel 1: best substitution, or best indel 2: best edit overall (suggestion that you reduce i and d for performance)'
+  - names:
+      - -s
+    argument: "{0,1}"
+    description: SNV mode. Overrides draft k-mer checks, forcing reassessment at each position (-s 1 = yes, default = 0, no)
+  - names:
+      - -l
+    argument: FILE
+    description: input VCF file with annotated variants (e.g., clinvar.vcf), OPTIONAL
+  - names:
+      - -a
+    argument: '{0,1}'
+    description: soft masks missing k-mer positions having no fix (-v 1 = yes, default = 0, no)
+  - names:
+      - -v
+    argument: '{0,1}'
+    description: verbose mode (-v 1 = yes, default = 0, no)
+  - names:
+      - --help
+    argument: ""
+    description: display this message and exit
+  - names:
+      - --version
+    argument: ""
+    description: output version information and exit
+version: ntEdit v1.4.3