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
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
Edit this file to update this information.
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.