Task: getref

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.

Usage

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.

Note: The ncbi option is only available from Ariba release v2.14.0.

Options

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.