Description

GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false, assembler:‘spades’ ]

bins/*:file

A list of one or more bins in FASTA format for classification

*.{fasta,fna,fas,fa}{,.gz}

db_name:string

The name of the GTDB database to use.

db:file

Path to a directory containing a GDTB database, as uncompressed from from the ‘full package’ gtdbdtk_data.tar.gz file. You can give the ‘release’ directory here. Must contain the ‘metadata’ subdirectory

release[0-9]+/

use_pplacer_scratch_dir:boolean

Set to true to reduce pplacer memory usage by writing to disk (slower)

mash_db:file

The local copy of the Mash sketch database used by GTDB-tk if ani_screen mode is used (optional)

*.msh

Output

name:type
description
pattern

gtdb_outdir

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false, assembler:‘spades’ ]

*

${prefix}:map

All files output by GTDB-Tk

*

summary

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false, assembler:‘spades’ ]

*.{summary.tsv}

${prefix}/classify/*.summary.tsv:map

A TSV summary file for the classification

*.{summary.tsv}

tree

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{classify.tree}

${prefix}/classify/*.classify.tree:map

Groovy Map NJ or UPGMA trees in Newick format produced from a multiple sequence alignment

*.{classify.tree}

markers

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{markers_summary.tsv}

${prefix}/identify/*.markers_summary.tsv:map

A TSV summary file lineage markers used for the classification.

*.{markers_summary.tsv}

msa

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{msa.fasta.gz}

${prefix}/align/*.msa.fasta.gz:map

Multiple sequence alignments file.

*.{msa.fasta.gz}

user_msa

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{user_msa.fasta.gz}

${prefix}/align/*.user_msa.fasta.gz:map

Multiple sequence alignments file for the user-provided files.

*.{user_msa.fasta.gz}

filtered

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{filtered.tsv}

${prefix}/align/*.filtered.tsv:map

A list of genomes with an insufficient number of amino acids in MSA

*.{filtered.tsv}

failed

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{failed_genomes.tsv}

${prefix}/identify/*.failed_genomes.tsv:map

A TSV summary of the genomes which GTDB-tk failed to classify.

*.{failed_genomes.tsv}

log

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{log}

${prefix}/${prefix}.log:map

GTDB-tk log file

*.{log}

warnings

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}/${prefix}.warnings.log:map

GTDB-tk warnings log file

*.{warnings.log}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

gtdbtk
GNU General Public v3 (GPL v3)

GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.

ecogenomics.github.io/GTDBTk https://github.com/Ecogenomics/GTDBTk 10.1093/bioinformatics/btz848
mag
Github user skrakau
Github user abhi18av
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