anvi-run-ncbi-cogs

This program runs NCBI's COGs to associate genes in an anvi'o contigs database with functions. COGs database was been designed as an attempt to classify proteins from completely sequenced genomes on the basis of the orthology concept..

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Authors

Can consume

contigs-db cogs-data

Can provide

functions

Usage

This program annotates genes in your contigs-db with functions using NCBI’s Clusters of Orthologus Groups (COGs) database.

This program assumes that the user has successfully set up the COGs database on their computer using the anvi’o program anvi-setup-ncbi-cogs.

The only critical parameter to anvi-run-ncbi-cogs is a contigs-db. The program will store its output in the contigs-dbas a functions artifact.

If the cogs-data was stored at a specific path when anvi-setup-ncbi-cogs was run, then providing that path using the --cog-data-dir parameter is also necessary.

Without the flag --cog-data-dir, anvi’o will just search in the default location.

You can also use blastp to search, by running:

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.