anvi-setup-trna-taxonomy [program]

The purpose of this program is to setup necessary databases for tRNA genes collected from GTDB (https://gtdb.ecogenomic.org/), genomes in your local anvi'o installation so taxonomy information for a given set of tRNA sequences can be identified using anvi-run-trna-taxonomy and made sense of via anvi-estimate-trna-taxonomy).

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Can provide

trna-taxonomy-db

Can consume

Usage

This program downloads a local copy of a subset of the databases from GTDB (stored in a trna-taxonomy-db), so that tRNA sequences in your dataset can be associated with taxonomy information. It is required to run this program before you can run anvi-run-trna-taxonomy or anvi-estimate-trna-taxonomy.

Like other anvi-setup- programs, this only needs to be run once per anvi’o version. The default path is anvio/data/misc/TRNA-TAXONOMY. You can store the resulting trna-taxonomy-db in a custom location if desired), but then you’ll need to provide the path to it whenever you run anvi-run-trna-taxonomy.

To run this program, you can simply run

If you are trying to redownload these databases, run:

Alternatively, you can use --redo-databases if you just want to update the database version without redownloading the data.

Edit this file to update this information.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.