searchindex.js

Search.setIndex({"alltitles": {"Abundances estimates (experimental)": [[7, "abundances-estimates-experimental"]], "Abundances in the Centrifuge report format": [[7, "abundances-in-the-centrifuge-report-format"]], "Abundances in the Kraken report format": [[7, "abundances-in-the-kraken-report-format"]], "Abundances in the MetaPhlAn2 report format": [[7, "abundances-in-the-metaphlan2-report-format"]], "Adjusting the PATH variable": [[8, "adjusting-the-path-variable"]], "Analyzing read assignments": [[5, null]], "Assignments": [[7, "assignments"]], "Build a tree": [[4, "build-a-tree"]], "Build the index": [[4, "build-the-index"]], "Building a custom database": [[4, null]], "Building a custom database with RefSeq genomes and the NCBI taxonomy": [[4, "building-a-custom-database-with-refseq-genomes-and-the-ncbi-taxonomy"]], "Building a custom database with user-provided data": [[4, "building-a-custom-database-with-user-provided-data"]], "Building a standard database": [[10, null]], "Centrifuge format": [[7, "id27"]], "Classifying reads": [[0, null]], "Command-line interface": [[1, null]], "Compressed ProPhyle index": [[7, "id29"]], "Compressed ProPhyle index for transmission": [[7, "compressed-prophyle-index-for-transmission"]], "Compressing indexes for transmission": [[2, null]], "Compression": [[2, "compression"]], "Decompression": [[2, "decompression"]], "Download sequences from NCBI": [[4, "download-sequences-from-ncbi"]], "Downloading genomes": [[10, "downloading-genomes"]], "Example": [[7, "example"], [7, "id14"]], "Examples": [[7, "examples"], [7, "id7"]], "File formats": [[7, null]], "Index construction": [[10, "index-construction"]], "Input data formats": [[7, "input-data-formats"]], "Installing ProPhyle": [[8, null]], "Installing ProPhyle using Bioconda": [[8, "installing-prophyle-using-bioconda"]], "Installing ProPhyle using PIP": [[8, "installing-prophyle-using-pip"]], "Installing dependencies": [[8, "installing-dependencies"]], "Internal ProPhyle formats": [[7, "internal-prophyle-formats"]], "Introduction": [[7, "introduction"], [7, "id1"], [7, "id3"], [7, "id5"], [7, "id8"], [7, "id10"], [7, "id12"], [7, "id16"], [7, "id18"]], "Kraken report format": [[7, "id25"]], "Kraken-like format": [[7, "id24"]], "Metaphlan 2 report format": [[7, "id26"]], "NHX attributes": [[7, "id20"]], "NHX trees": [[7, "nhx-trees"]], "Newick trees": [[7, "newick-trees"]], "ProPhyle Index": [[7, "index-6"]], "ProPhyle SAM fields": [[7, "id22"]], "ProPhyle SAM headers": [[7, "id21"]], "ProPhyle SAM tags": [[7, "id23"]], "ProPhyle documentation contents": [[3, null]], "ProPhyle index": [[7, "id28"]], "ProPhyle \u2013 the main program": [[1, "prophyle-the-main-program"]], "Quick example": [[6, null]], "Read assignments in SAM/BAM": [[7, "read-assignments-in-sam-bam"]], "Read assignments in a Kraken-like format": [[7, "read-assignments-in-a-kraken-like-format"]], "Requirements": [[9, null]], "Running ProPhyle directly from the repository": [[8, "running-prophyle-directly-from-the-repository"]], "Sequences": [[7, "sequences"]], "Specification": [[7, "specification"], [7, "id2"], [7, "id4"], [7, "id6"], [7, "id9"], [7, "id11"], [7, "id13"], [7, "id17"], [7, "id19"]], "prophyle": [[1, "prophyle"]], "prophyle classify": [[1, "prophyle-classify"]], "prophyle compress": [[1, "prophyle-compress"]], "prophyle decompress": [[1, "prophyle-decompress"]], "prophyle download": [[1, "prophyle-download"]], "prophyle index": [[1, "prophyle-index"]], "prophyle_assembler": [[1, "prophyle-assembler"]], "prophyle_assignment": [[1, "prophyle-assignment"]], "prophyle_index": [[1, "id1"]], "prophyle_propagation_makefile.py": [[1, "prophyle-propagation-makefile-py"]], "prophyle_propagation_postprocessing.py": [[1, "prophyle-propagation-postprocessing-py"]], "prophyle_propagation_preprocessing.py": [[1, "prophyle-propagation-preprocessing-py"]], "prophyle_validate_tree.py": [[1, "prophyle-validate-tree-py"]]}, "docnames": ["classify", "cli", "compress", "contents", "custom_db", "deprec/analyze", "example", "formats", "install", "requirements", "standard_db"], "envversion": {"sphinx": 63, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1}, "filenames": ["classify.rst", "cli.rst", "compress.rst", "contents.rst", "custom_db.rst", "deprec/analyze.rst", "example.rst", "formats.rst", "install.rst", "requirements.rst", "standard_db.rst"], "indexentries": {"bam": [[7, "index-2", false]], "centrifuge report": [[7, "index-5", false]], "compression": [[2, "index-0", false]], "cpu": [[9, "term-CPU", true]], "disk space": [[9, "term-Disk-space", true]], "example": [[6, "index-0", false]], "kraken report": [[7, "index-3", false]], "memory": [[9, "term-Memory", true]], "metaphlan report": [[7, "index-4", false]], "ncbi": [[10, "index-0", false]], "newick": [[7, "index-0", false]], "nhx": [[7, "index-1", false]], "operating system": [[9, "term-Operating-system", true]], "prophyle compressed index": [[7, "index-7", false]], "prophyle index": [[7, "index-6", false]], "refseq": [[10, "index-0", false]], "sam": [[7, "index-2", false]]}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": [1, 4, 6, 7, 8], "0": [1, 4, 6, 7], "1": [1, 4, 7], "10": [4, 6, 7], "100": 7, "11": [4, 7], "1111111000111": 7, "11111110111": 7, "12": 4, "14": 9, "15": 1, "1x3": 7, "2": [4, 9], "20": 4, "25": [6, 10], "3": [1, 4, 7, 8, 9], "31": [1, 10], "32": 4, "36870": 7, "37": 7, "3x3": 7, "4": [1, 7, 8, 9], "5": 7, "561": 6, "562": 1, "5964": 7, "5981": 7, "6": [4, 7], "60": 7, "7": [4, 7], "703004": 7, "8": [7, 8, 9], "9": 7, "A": [1, 2, 4, 7], "For": [0, 2, 4, 7, 9], "If": [2, 7, 10], "It": [7, 8], "OFS": 4, "Such": 9, "The": [0, 4, 7, 8, 9, 10], "There": [8, 10], "These": 10, "To": [2, 7, 8, 10], "_": 4, "_index_ecoli": 6, "about": 4, "abov": [0, 4], "absolut": 7, "abund": 3, "acc2taxid": 4, "access": 4, "accord": 4, "acgt": 7, "activ": [8, 10], "ad": 7, "adapt": 4, "add": [1, 4, 6, 8], "adjust": 7, "advanc": 1, "after": 7, "again": 7, "against": 1, "algorithm": 1, "alia": 8, "align": 1, "all": [1, 2, 4, 7, 8, 9, 10], "alreadi": 1, "also": [7, 8, 10], "amb": 7, "ambigu": 7, "amili": 7, "an": [2, 4, 6, 7], "analyz": 1, "ani": [4, 7, 9], "ann": 7, "annot": 1, "anoth": 8, "appear": 10, "approach": 8, "approxim": 9, "ar": [0, 1, 4, 7, 8, 10], "archaea": [4, 7], "archiv": [1, 2, 7], "argument": 1, "arrai": [2, 7, 10], "artifici": 4, "asm": 4, "assembl": [1, 7], "assembli": 4, "assembly_summari": 4, "assign": [0, 1, 3, 4], "associ": [4, 7], "attribut": 4, "augment": 10, "author": 1, "auto": 1, "autocomplet": [1, 4, 7], "automat": [1, 7, 8], "auxiliari": [1, 7, 8], "avail": 4, "awk": 4, "b": 1, "bacteri": [4, 6, 9, 10], "bacteria": [1, 4, 6, 7, 10], "bandwidth": 4, "base": [1, 2, 7, 10], "becom": 10, "befor": [1, 7], "begin": 4, "bin": 8, "bioconda": [3, 6], "bit": [2, 7], "border": 1, "branch": 7, "brevipalpi": 7, "brinda": 1, "build": [1, 3, 6], "built": 4, "burrow": 7, "bv": 1, "bwa": 7, "bwt": 7, "bwtupdat": 7, "c": [1, 7, 8], "c1": [1, 7], "c2": [1, 7], "c__": 7, "call": [8, 10], "can": [0, 1, 2, 4, 7, 8, 9, 10], "cat": 8, "cellular": 7, "cf": 7, "chang": 4, "channel": [6, 8], "charact": 7, "check": 1, "children": 7, "choic": 4, "chromosom": 1, "cigar": 7, "clade": 7, "class": 7, "classif": [1, 7], "classifi": [3, 6, 7], "clon": 8, "clone": 8, "code": 7, "coli": 6, "collis": 10, "column": 7, "com": [1, 8], "combin": 7, "come": 10, "comma": 7, "comma_delimited_list_of_nod": 7, "command": [0, 3, 4, 10], "commit": 7, "commun": 7, "compil": [1, 8], "complet": [4, 7], "complex": [1, 10], "composit": 7, "compress": 3, "comput": [1, 7], "conda": [6, 8], "condit": 4, "config": [6, 8], "configur": 1, "construct": [0, 1, 3, 7], "consumpt": 9, "contact": 1, "contain": [2, 4, 7, 10], "contig": [1, 7, 9], "contig_id": 7, "copi": 10, "core": [4, 9, 10], "correspond": [4, 7, 9], "count": 1, "cover": 7, "coverag": [1, 7], "cpu": [9, 10], "creat": [1, 2, 4, 7, 8], "cttngttt": 7, "curent": 7, "current": 8, "custom": 3, "cut": 4, "d": [1, 7, 10], "data": 3, "databas": [1, 3, 6, 9], "db": 4, "deactiv": 10, "decompress": 3, "deduc": 0, "default": [6, 8, 10], "delimit": 7, "deprec": [4, 7], "deriv": [2, 7], "descript": 7, "detect": 1, "dictionari": 1, "dir": [1, 2, 10], "dir_with_genom": 4, "directli": [3, 7], "directori": [1, 4, 7, 8, 10], "discard": 7, "disk": 9, "dist": 7, "distanc": 1, "distribut": 8, "divid": 7, "do": 1, "doe": [7, 9], "download": [3, 6], "dure": 7, "dustmask": [1, 10], "e": [4, 6, 7], "each": [4, 7], "easi": 4, "ecoli": 1, "edu": 1, "either": 8, "encod": 7, "endosymbiont": 7, "ensur": [4, 10], "entir": [2, 10], "enu": 7, "environ": 8, "equal": 7, "equival": [1, 7], "estim": [3, 9], "et": 4, "etc": [7, 10], "ete3": [7, 8], "everi": 1, "exampl": [1, 3], "execut": [8, 10], "exist": 1, "exit": 1, "experiment": [1, 3], "export": 8, "extract": [1, 4, 7], "f": [1, 4, 7], "f1": 1, "f2": 1, "f__": 7, "fa": [1, 4, 7, 9], "faidx": 4, "fake": 7, "famili": 7, "faq": 4, "fast": 1, "fasta": [1, 4, 7, 9], "fastapath": 7, "fastq": [1, 7], "featur": 2, "field": 4, "file": [1, 2, 3, 4, 9, 10], "filenam": [2, 4], "filesuffix": 4, "filter": 10, "final": 7, "find": 4, "finish": 0, "first": [1, 4, 8], "five": 9, "flag": 7, "float": [1, 7], "fna": 4, "follow": [4, 7, 8], "forc": 1, "forg": [6, 8], "form": 7, "format": [0, 1, 2, 3, 4], "forth": 7, "found": 4, "fq": [0, 1, 6], "fr": 1, "from": [0, 1, 2, 3, 6, 7, 9, 10], "ftp": 4, "ftpdir": 4, "ftpfilepath": 4, "ftpselect": 4, "full": 7, "further": 4, "fx": 1, "g": [1, 4, 7, 8, 10], "g1": 1, "g2": 1, "g__": 7, "gb": 9, "gcc": [8, 9], "gener": 1, "genom": [1, 3, 6, 7], "genome1": 4, "genu": 7, "get": 4, "git": 8, "github": 8, "glossina": 7, "glossinidia": 7, "gmail": 1, "gnu": 4, "go": 10, "greedi": 1, "gregori": 1, "gunzip": 4, "gz": [1, 2, 4, 7], "h": 1, "h1": [1, 7], "h2": [1, 7], "hampshir": 7, "harvard": 1, "have": [4, 9], "hc": 7, "hd": 7, "help": 1, "here": 4, "hf": 7, "hierarch": 7, "higher": 7, "hit": [1, 7], "hmp": 1, "home": 4, "hour": 10, "hsph": 1, "http": 8, "hylum": 7, "i": [0, 1, 2, 4, 7, 8, 10], "id": 7, "ident": 7, "identifi": 4, "igiiiihi": 7, "ignor": 7, "ii": 7, "impl": 1, "implement": 1, "in_tre": 1, "includ": [2, 4, 7], "incorpor": 1, "increment": 7, "indent": 7, "index": [0, 3, 6, 9], "index_dir": [0, 4], "indic": 7, "infer": 7, "info": 4, "inform": [1, 2, 4], "ingdom": 7, "input": [1, 3], "instal": [3, 6, 10], "instanc": [7, 9, 10], "instead": [4, 7], "int": [1, 7, 10], "integ": 7, "interest": 4, "interfac": 3, "intern": [1, 3, 4], "internet": 2, "intersect": 1, "its": [7, 8], "j": [1, 4, 10], "job": 4, "json": [1, 7], "k": [0, 1, 2, 4, 6, 7, 10], "k__": 7, "kamil": 1, "karel": 1, "kbrinda": 1, "keep": 1, "kindom": 7, "kingdom": 7, "klcp": 7, "kmer": 7, "kmer_length": 4, "kmercount": 7, "kmers_ful": 7, "kmers_reduc": 7, "kraken": 1, "kucherov": 1, "l": [1, 4], "lass": 7, "latest": 4, "lca": 1, "lcp": [1, 2, 7, 10], "ldot": 7, "leaf": [4, 7], "leav": [4, 7], "left": 7, "lenght": 7, "length": [0, 1, 7, 9, 10], "level": 7, "lexigraph": 7, "librari": [1, 4, 7, 8, 10], "library_main_dir": 4, "library_nam": 4, "like": [9, 10], "line": 3, "lineag": 4, "link": 4, "list": [7, 8], "ln": 7, "log": [1, 7], "log_fil": 4, "look": 10, "low": [1, 10], "m": [1, 10], "mai": 8, "main": [3, 4, 7, 8], "make": 7, "makefil": 1, "mani": 1, "map": 7, "mapq": 7, "mask": [1, 7], "master": 7, "match": [1, 4, 7], "mean": 7, "measur": [1, 7], "memori": 9, "mer": [0, 1, 6, 7, 10], "merg": [1, 7, 10], "merge_root": 7, "messag": 1, "metagenom": [1, 7], "microbi": 7, "might": [1, 8, 10], "mimic": 1, "miniconda": 8, "minim": 7, "miss": 8, "mlv": 1, "mode": 1, "modifi": 4, "moment": 4, "more": 4, "much": 10, "multi": 7, "multipl": [1, 8, 10], "multipli": 9, "must": [1, 7], "my_bv_index": [0, 10], "my_read": 0, "n": 8, "n1": 7, "n2": 7, "n3": 7, "n4": 7, "n5": 7, "n6": 7, "name": [1, 2, 4, 7, 10], "named_lineag": 4, "ncbi": [3, 6, 7, 10], "nclassifi": 7, "necessari": [2, 4], "need": 8, "new": 7, "newick": [1, 4, 10], "newli": 4, "nhx": [1, 10], "node": [1, 4, 7, 10], "node_nam": [1, 7], "non": 7, "norm": 1, "normal": 7, "note": [1, 8], "nucleotid": 7, "number": [1, 4, 7, 9, 10], "numer": 10, "numread": 7, "numuniqueread": 7, "nw": [1, 4, 6, 7, 10], "o": [1, 7], "o1": 7, "o2": 7, "o__": 7, "obtain": 9, "occ": 7, "omain": 7, "onc": 10, "one": 4, "onli": [1, 7], "oper": [8, 9], "option": [1, 2, 4, 8], "order": 7, "origin": [7, 9], "other": [4, 7, 10], "otherwis": [0, 7, 10], "otu": 7, "out": 1, "out_tre": 1, "output": [1, 2, 7], "output_fil": 4, "over": 2, "p": [1, 7, 10], "p1": 7, "p__": 7, "pac": 7, "pack": 7, "packag": 8, "parallel": [1, 4], "paramet": [1, 4, 7, 10], "parent": 4, "pars": 7, "particular": 9, "path": [1, 4, 7], "pe": 8, "peci": 7, "percentag": 7, "perl": 8, "pg": 7, "phylip": 7, "phylogenet": [1, 4, 7], "phylogeni": 1, "phylum": 7, "pignotti": 1, "pip": 3, "place": [4, 10], "plasmid": [1, 10], "pleas": [4, 10], "pnext": 7, "po": 7, "posit": [1, 7], "possibl": 8, "postprocess": 1, "prebuild": 10, "prefix": [1, 7, 10], "preliminari": 7, "prepend": [4, 8, 10], "present": 7, "prevent": 10, "previou": [7, 10], "print": [1, 4], "profil": 7, "program": [3, 8, 10], "propag": [1, 7, 9], "prophyl": [0, 2, 4, 6, 9, 10], "prophyle_assembl": 3, "prophyle_assign": 3, "prophyle_index": 3, "prophyle_merge_tre": 1, "prophyle_ncbi_tre": 4, "prophyle_propagation_makefil": 3, "prophyle_propagation_postprocess": 3, "prophyle_propagation_preprocess": 3, "prophyle_validate_tre": 3, "proport": 7, "provid": [2, 3, 7], "pseudo": 7, "put": 4, "pwd": 8, "py": [3, 4, 8], "pypi": 8, "python": [8, 9], "pythonuserbas": 8, "qname": 7, "qual": 7, "qualiti": [1, 7], "queri": [1, 7, 10], "quick": 3, "randomli": 6, "rang": 7, "rank": [4, 7], "rate": 1, "rder": 7, "re": 1, "read": [1, 3, 6], "read3": 7, "reads1": 1, "reads2": 1, "recommend": 8, "reconstruct": 2, "record": 1, "recurs": 8, "reduc": 7, "refer": [4, 7], "refseq": [3, 6, 9, 10], "region": [1, 10], "rel": [4, 7], "repeat": 1, "replac": [1, 10], "report": 0, "repositori": 3, "repres": 7, "requir": [3, 4, 8], "reserv": 7, "respect": [4, 7], "restart": 1, "result": [1, 6, 10], "revers": 7, "revis": 7, "rewrit": 1, "right": 7, "rname": 7, "rnext": 7, "root": 7, "roughli": 9, "run": [3, 4, 10], "s__": 7, "sa": [1, 7], "salikhov": 1, "sam": [0, 1, 6], "same": [1, 4, 8], "sampl": [1, 2, 7], "samtool": 4, "save": [1, 4], "sci_nam": 4, "scientif": 7, "score": 1, "script": [4, 8], "search": 1, "second": [1, 7], "section": 2, "see": [2, 7], "select": [4, 6], "separ": [4, 7, 8], "seq": 7, "sequenc": 1, "serv": 10, "server": 4, "set": [1, 8, 10], "sever": [7, 10], "share": 7, "should": [4, 7, 10], "show": 1, "silent": 1, "similar": 7, "simon": 1, "simpli": 7, "simplifi": 2, "sinc": [4, 7], "singl": 7, "situat": 10, "size": [1, 6, 7, 9, 10], "skip": 1, "slightli": 10, "slower": 10, "smaller": 10, "sn": 7, "so": [7, 8, 10], "solut": 4, "some": 8, "sourc": 8, "sp": 7, "space": [7, 9], "speci": [4, 7], "specif": [1, 2], "specifi": [0, 7, 10], "split": 4, "sq": 7, "standard": [1, 3, 4], "start": 7, "statist": [1, 7], "str": 1, "strain": [4, 7], "string": 7, "subcommand": 1, "subdirectori": 4, "submodul": 8, "subset": [4, 7], "subtract": 1, "subtre": [1, 6], "suffici": 4, "suffix": [2, 7], "sum": 7, "summari": 4, "support": 7, "sure": 7, "system": [8, 9], "t": [1, 4], "tab": 4, "tabl": 7, "take": 10, "tar": [1, 2, 7], "tax": 1, "taxid": [4, 6, 7], "taxon": 7, "taxonom": [4, 7], "taxonomi": [3, 6, 7, 10], "taxrank": 7, "temporari": 1, "than": 7, "thei": [1, 7, 10], "them": [1, 4, 7, 8], "therefor": [4, 8, 10], "thi": [1, 2, 4, 7, 10], "thread": 1, "three": 8, "through": 7, "thu": 7, "tie": 1, "time": [1, 4], "tlen": 7, "tool": 7, "toolkit": 4, "total": 9, "transform": 7, "transmiss": 3, "treat": 7, "tree": [1, 10], "tree_1": 4, "tree_2": 4, "try": 10, "tsv": [1, 4, 7], "two": [1, 9], "txt": [1, 4, 7, 8], "type": 7, "typic": 7, "u": [1, 7, 8], "unclassifi": 7, "uniqu": [4, 7], "univ": 1, "unix": [8, 9], "unknown": 7, "unless": [0, 4, 10], "unus": 7, "up": [7, 8], "up1": 7, "up2": 7, "upon": 8, "ur": 7, "us": [0, 1, 3, 4, 6, 7, 10], "usag": 1, "user": [3, 8], "usual": 4, "v": [1, 4], "valu": 7, "verbos": 1, "veri": 4, "verifi": 1, "version": [1, 7], "viral": [4, 10], "virus": [1, 10], "wa": 8, "wai": [4, 8], "we": 4, "websit": 7, "wget": 4, "wheeler": 7, "when": [0, 1, 8], "where": [4, 7, 10], "whether": 1, "which": [4, 8], "wigglesworthia": 7, "wikipedia": 7, "without": 7, "work": 4, "would": [0, 10], "written": 8, "x": [1, 7], "xarg": 8, "you": [0, 4, 8], "your": [0, 4, 6, 8, 10], "zlib": 8}, "titles": ["<span class=\"section-number\">6. </span>Classifying reads", "<span class=\"section-number\">9. </span>Command-line interface", "<span class=\"section-number\">7. </span>Compressing indexes for transmission", "ProPhyle documentation contents", "<span class=\"section-number\">5. </span>Building a custom database", "Analyzing read assignments", "<span class=\"section-number\">1. </span>Quick example", "<span class=\"section-number\">8. </span>File formats", "<span class=\"section-number\">3. </span>Installing ProPhyle", "<span class=\"section-number\">2. </span>Requirements", "<span class=\"section-number\">4. </span>Building a standard database"], "titleterms": {"2": 7, "abund": 7, "adjust": 8, "analyz": 5, "assign": [5, 7], "attribut": 7, "bam": 7, "bioconda": 8, "build": [4, 10], "centrifug": 7, "classifi": [0, 1], "command": 1, "compress": [1, 2, 7], "construct": 10, "content": 3, "custom": 4, "data": [4, 7], "databas": [4, 10], "decompress": [1, 2], "depend": 8, "directli": 8, "document": 3, "download": [1, 4, 10], "estim": 7, "exampl": [6, 7], "experiment": 7, "field": 7, "file": 7, "format": 7, "from": [4, 8], "genom": [4, 10], "header": 7, "index": [1, 2, 4, 7, 10], "input": 7, "instal": 8, "interfac": 1, "intern": 7, "introduct": 7, "kraken": 7, "like": 7, "line": 1, "main": 1, "metaphlan": 7, "metaphlan2": 7, "ncbi": 4, "newick": 7, "nhx": 7, "path": 8, "pip": 8, "program": 1, "prophyl": [1, 3, 7, 8], "prophyle_assembl": 1, "prophyle_assign": 1, "prophyle_index": 1, "prophyle_propagation_makefil": 1, "prophyle_propagation_postprocess": 1, "prophyle_propagation_preprocess": 1, "prophyle_validate_tre": 1, "provid": 4, "py": 1, "quick": 6, "read": [0, 5, 7], "refseq": 4, "report": 7, "repositori": 8, "requir": 9, "run": 8, "sam": 7, "sequenc": [4, 7], "specif": 7, "standard": 10, "tag": 7, "taxonomi": 4, "transmiss": [2, 7], "tree": [4, 7], "us": 8, "user": 4, "variabl": 8}})