gtdbtk_classifywf

Tags: taxonomy classification phylogeny gtdb bacteria archaea marker-genes sample-scope

Taxonomic classification of bacterial and archaeal genomes using GTDB-Tk.

Uses GTDB-Tk to assign objective taxonomic classifications to genome assemblies based on the Genome Taxonomy Database. It identifies marker genes, aligns them, and places the genome into the reference tree to determine taxonomy.

Database Required

Requires the massive GTDB-Tk database (~60GB+) to be available.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

db: Path

Name	Type	Description
db	Path	Path (or Set of paths) to the GTDB-Tk reference database

Outputs

record (
    meta: Record,
    bac_tsv: Path?,
    ar_tsv: Path?,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
bac_tsv	Path?	The bacterial classification summary file containing the taxonomic assignment
ar_tsv	Path?	The archaeal classification summary file containing the taxonomic assignment
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

GTDB Classify Parameters

Parameter	Type	Default	Description
--gtdb_min_af	number	0.65	Minimum alignment fraction to consider closest genome
--gtdb_min_perc_aa	integer	10	Filter genomes with an insufficient percentage of AA in the MSA
--force_gtdb	boolean	false	Continue processing if an error occurs on a single genome

Used By

Subworkflows

• gtdb - Taxonomic classification with the Genome Taxonomy Database.

Workflows

• gtdb - Identify marker genes and assign taxonomic classifications using GTDB.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• GTDB-Tk
  Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics (2019)

• pplacer
  Matsen FA, Kodner RB, Armbrust EV pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11, 538 (2010)

Source

View source on GitHub

Version

GTDBTK_CLASSIFYWF:
    - gtdbtk: 2.7.1