Microbial 'omics


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anvi-run-ncbi-cogs [program]

Run 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. It is no longer actively developed, however, it is still very effective for daily needs. You may want to consider Pfams or the eggNOG database for more comprehensive functional insights.

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

Table of Contents

Provides

functions

Requires or uses

contigs-db cogs-data

Usage

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

Before you run this program, you’ll have to set up the COGs database on your computer with the program anvi-setup-ncbi-cogs.

As mentioned above, the COGs database is no longer actively added to, so you might also want to consider using a separate database. As of yet, anvi’o does not have a program to accesss the eggNOG database (but instructions to use this database to get and import function information are here), but does have the functionality to use the Pfams database (check out anvi-run-pfams for more information) and the KOfamKOALA database (see anvi-run-kegg-kofams).

To run, you’ll need to provide a contigs-db. If you stored the cogs-data that you got from running anvi-setup-ncbi-cogs in a custom location, you’ll need to provide that path as well. The output is a functions artifact.

anvi-run-ncbi-cogs -c contigs-db \ --cog-data-dir path/to/cogs-data

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

By default, this program uses DIAMOND in the “fast” setting for database searching. To instead run in “sensitive” mode, just call:

anvi-run-ncbi-cogs -c contigs-db \ --sensitive

You can also use blastp to search, by running:

anvi-run-ncbi-cogs -c contigs-db \ --search-with blastp

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.