Microbial 'omics

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# 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).

See program help menu or go back to the main page of anvi’o programs and artifacts.

## 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.

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

anvi-setup-scg-taxonomy

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