anvi-run-ncbi-cogs

This program runs NCBI's COGs to associate genes in an anvi'o contigs database with functions. This program can also run NCBI's COGs to annotate an amino acid sequence with function. 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

cogs-data contigs-db fasta

Can provide

functions functions-txt

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.

This program requires one of two possible inputs a contigs-db or a fasta file of amino acid sequences. When a contigs-db is provided, the program will store its output in the contigs-db as a functions artifact. Otherwise you must specify an output file path using -o, to which the program will write a TAB-delimited file containing all the annotatons found in the input fasta file.

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.

Choosing a different database version

If you want to annotate your genes with a non-default version of cogs-data, provide that version after the --cog-version parameter:

Choosing a different search program

By default, this program uses diamond to search for hits to the database. 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.