Microbial 'omics


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anvi-run-kegg-kofams [program]

Run KOfam HMMs on an anvi'o contigs database.

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

Table of Contents

Provides

kegg-functions

Requires or uses

contigs-db kegg-db

Usage

anvi-run-kegg-kofams annotates a contigs-db with HMM hits from KOfam, a database of KEGG Orthologs (KOs). You must set up these HMMs on your computer using anvi-setup-kegg-kofams before you can use this program.

Briefly, what this program does is extract all the gene calls from the contigs-db and checks each one for hits to the KOfam HMM profiles in your kegg-db. This can be time-consuming given that the number of HMM profiles is quite large, and especially time-consuming if the number of genes in the contigs-db is also large. Multi-threading is a good idea if you have the computational capability to do so.

Many HMM hits will be found, most of them weak. The weak hits will by default be eliminated according to the score thresholds provided by KEGG; that is, only hits with scores above the threshold for a given KO profile will be annotated in the contigs-db. It is perfectly normal to notice that the number of raw hits found is many, many times larger than the number of annotated KO hits in your database.

In the contigs-db functions table, annotated KO hits (kegg-functions) will have the source KOfam.

Running this program is a pre-requisite for metabolism estimation with anvi-estimate-metabolism. Note that if you are planning to run metabolism estimation, it must be run with the same kegg-db that is used in this program to annotate KOfam hits.

Standard usage

anvi-run-kegg-kofams -c CONTIGS.db

Use a specific non-default KEGG data directory

anvi-run-kegg-kofams -c CONTIGS.db --kegg-data-dir /path/to/directory/KEGG

Run with multiple threads

anvi-run-kegg-kofams -c CONTIGS.db -T 4

Use a different HMMER program

By default, anvi-run-kegg-kofams uses hmmsearch to find KO hits. If for some reason you would rather use a different program (hmmscan is also currently supported), you can do so.

anvi-run-kegg-kofams -c CONTIGS.db --hmmer-program hmmscan

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.