bakta_download

Tags: bacteria database download annotation bakta setup run-scope

Download the Bakta annotation database.

Fetches the pre-compiled database required by Bakta for genome annotation. The database contains UniProt clusters, AMR genes, and other reference data needed for comprehensive bacterial genome annotation.

Internet & Storage Required

This process requires an active internet connection and significant disk space to store the database files. The 'light' database is ~1.5GB, while the 'full' database is ~30GB uncompressed.

Outputs

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

Field	Type	Description
db	Path?	The Bakta database directory containing annotation reference data
db_tarball	Path?	A compressed tarball of the database (if requested via parameters)
logs	Set<Path?>	Optional program specific log files

Parameters

Bakta Download Parameters

Parameter	Type	Default	Description
--bakta_db	string		Tarball or path to the Bakta database
--bakta_db_type	string	full	Which Bakta DB to download 'full' (~30GB) or 'light' (~2GB) (choices: full, light)
--bakta_save_as_tarball	boolean	false	Save the Bakta database as a tarball
--download_bakta	boolean	false	Download the Bakta database to the path given by --bakta_db

Used By

Subworkflows

• bakta - Rapid bacterial genome annotation.

Workflows

• bactopia - Comprehensive bacterial analysis pipeline for complete genomic characterization.
• bakta - Rapid annotation of bacterial genomes and plasmids.
• staphopia - Comprehensive analysis pipeline for Staphylococcus aureus isolates.

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)

• Bakta
  Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A Bakta - rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbial Genomics 7(11) (2021)

Source

View source on GitHub

Version

BAKTA_DOWNLOAD:
    - bakta: 1.12.0