anvi-setup-scg-taxonomy [program]

The purpose of this program is to download necessary information from GTDB (https://gtdb.ecogenomic.org/), and set it up in such a way that your anvi'o installation is able to assign taxonomy to single-copy core genes using anvi-run-scg-taxonomy and estimate taxonomy for genomes or metagenomes using anvi-estimate-scg-taxonomy).

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Authors

Can consume

This program seems to know what its doing. It needs no input material from its user. Good program.

Can provide

scgs-taxonomy-db

Usage

This program downloads and sets up the search databases used for the scg-taxonomy workflow (from GTDB) so that you can run anvi-run-scg-taxonomy and anvi-estimate-scg-taxonomy. This program generates a scgs-taxonomy-db artifact, which is required to run both of those programs.

For more information on that workflow, check out this page

You will only have to run this program once per anvi’o installation.

Why is this not done by default? It just makes things easier downstream to build these databases with the DIAMOND installed on your computer to avoid incompatibility issues. Besides, it should take under a minute and is as simple as running

If you have already already run this program and are trying to redownload this data, run

You can also download a specific release of this database by providing its URL with the flag --scg-taxonomy-remote-database-url.

Edit this file to update this information.

Additional Resources

• Usage examples and warnings

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.