Microbial 'omics


Brought to you by

anvi-setup-ncbi-cogs [program]

Download and setup NCBI's Clusters of Orthologous Groups database.

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

Table of Contents

Provides

cogs-data

Requires or uses

Usage

This program downloads and organizes a local copy of the data from NCBI’s COGs database for use in function annotation. This program generates a cogs-data artifact, which is required to run the program anvi-run-ncbi-cogs.

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).

Set up COGs data

anvi-setup-ncbi-cogs --just-do-it

If you already have a cogs-data artifact and are trying to redownload this data, run

anvi-setup-ncbi-cogs --reset

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.