ariba_getref
Tags: bacteria database download antimicrobial-resistance virulence ariba setup run-scope
Download and prepare reference databases for ARIBA analysis.
Uses ARIBA to fetch curated reference databases
(e.g., CARD, ResFinder, VFDB, PlasmidFinder) and prepare them for local assembly-based
gene detection. The database is indexed and packaged into a tarball for use with ariba run.
This process requires an active internet connection to fetch the specified database.
Inputs
db_name: String
| Name | Type | Description |
|---|---|---|
db_name | String | Name of the database to download (e.g., 'card', 'resfinder', 'vfdb_core', 'plasmidfinder') |
Outputs
record (
db: Path,
logs: Set<Path?>
)
| Field | Type | Description |
|---|---|---|
db | Path | A compressed tarball containing the prepared ARIBA database |
logs | Set<Path?> | Optional program specific log files |
Parameters
Used By
Subworkflows
- ariba - Rapidly identify genes by creating local assemblies from paired-end reads.
Workflows
- ariba - Gene identification through local assemblies.
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) -
Ariba
Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA, Harris SR ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb Genom 3, e000131 (2017) -
MEGARes
Lakin SM, Dean C, Noyes NR, Dettenwanger A, Ross AS, Doster E, Rovira P, Abdo Z, Jones KL, Ruiz J, Belk KE, Morley PS, Boucher C MEGARes: an antimicrobial resistance database for high throughput sequencing. Nucleic Acids Res. 45, D574-D580 (2017) -
SRST2
Inouye M, Dashnow H, Raven L-A, Schultz MB, Pope BJ, Tomita T, Zobel J, Holt KE SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 6, 90 (2014) -
VirulenceFinder
Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J. Clin. Microbiol. 52, 1501-1510 (2014)
Source
Version
ARIBA_GETREF:
- ariba: 2.14.7