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kpepper edited this page Jun 6, 2019 · 14 revisions

Task: getref

This downloads a reference dataset from one of:

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|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.

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