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Task: getref
kpepper edited this page Jun 6, 2019
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This downloads a reference dataset from one of:
- ARG-ANNOT. PMID: 24145532
- CARD. PMID: 23650175
- MEGARes PMID: 27899569
- NCBI BioProject: PRJNA313047
- plasmidfinder PMID: 24777092
- resfinder. PMID: 22782487
- VFDB. PMID: 26578559
- SRST2's version of ARG-ANNOT. PMID: 25422674.
- VirulenceFinder PMID: 24574290.
If you use one of the above resources, please cite it.
The usage is:
ariba getref reference_name output_prefix
where reference_name is one of: argannot, card, ncbi, megares, plasmidfinder, resfinder,
srst2_argannot, vfdb_core, vfdb_full, virulencefinder.
For example, to download the CARD data:
ariba getref card out.card
The output of getref is used as input to the task
[[prepareref|Task:-prepareref]].
Note: The ncbi option is only available from Ariba release v2.14.0.
For CARD and MEGARes you can use the option --version to download a specific version of the database. If not used, then the latest version will be downloaded.