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

, assembler:‘spades’ ]

bins (file)

The binned fasta files from the assembler

*.{fasta,fa}

database (file)

The local copy of the taxonomic database used by GTDB-tk (unzipped copy)

*

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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

summary (file)

A TSV summary file for the classification

*.{summary.tsv}

tree (file)

NJ or UPGMA tree in Newick format produced from a multiple sequence alignment

*.{classify.tree.gz}

markers (file)

A TSV summary file lineage markers used for the classification.

*.{markers_summary.tsv}

msa (file)

Multiple sequence alignments file.

*.{msa.fasta.gz}

user_msa (file)

Multiple sequence alignments file for the user-provided files.

*.{user_msa.fasta.gz}

filtered (file)

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

*.{filtered.tsv}

log (file)

GTDB-tk log file

*.{log}

warnings (file)

GTDB-tk warnings log file

*.{warnings.log}

failed (file)

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

*.{failed_genomes.tsv}
included in
mag
authors
Github user skrakau Github user abhi18av
get in touch
Ask a question on Slack Open an issue on GitHub

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