gtdbtk_download

Tags: gtdb taxonomy database download setup bacteria archaea sample-scope

Download and configure the GTDB-Tk reference database.

Uses the official download-db.sh script to fetch the latest Genome Taxonomy Database (GTDB) files required by GTDB-Tk. It automatically uncompresses the data and verifies the installation using gtdbtk check_install.

Internet & Storage Required

This process requires an active internet connection and significant disk space (~60GB+ uncompressed) to store the database files.

Outputs

record (
    db: Path?,
    db_tarball: Path?,
    logs: Set<Path?>
)

Field	Type	Description
db	Path?	The directory containing the uncompressed GTDB-Tk database files
db_tarball	Path?	A compressed tarball of the database (if requested via parameters)
logs	Set<Path?>	Optional program specific log files

Parameters

GTDB-Tk Setup Database Parameters

Parameter	Type	Default	Description
--gtdb	string		Tarball or path of a GTDB database. If a database is not found, you must use '--download_gtdb'
--download_gtdb	boolean	false	Download the latest GTDB database, even it exists
--gtdb_save_as_tarball	boolean	false	Download the latest GTDB database, and save it in a single tarball

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)

Source

View source on GitHub

Version

GTDBTK_DOWNLOAD:
    - gtdbtk: 2.7.1