Microbial 'omics


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anvi-setup-kegg-kofams [program]

Download and setup KEGG KOfam HMM profiles.

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

Table of Contents

Provides

kegg-db

Requires or uses

Usage

anvi-setup-kegg-kofams downloads and organizes data from KEGG for use by other programs, namely anvi-run-kegg-kofams and anvi-estimate-metabolism. It downloads HMM profiles from the KOfams database as well as metabolism information such as that stored in the KEGG MODULES resource. The program generates a directory with this data (kegg-db), which by default is located at anvio/anvio/data/misc/KEGG/.

Set up KEGG data

anvi-setup-kegg-kofams

Set up KEGG data in non-default location

anvi-setup-kegg-kofams --kegg-data-dir /path/to/directory/KEGG

An important thing to note about this program is that it has rigid expectations for the format of the KEGG data that it works with. Future updates to KEGG may break things such that the data can no longer be directly obtained from KEGG or properly processed. In the event that this happens, this program still has you covered. You can provide an archived KEGG data directory to the script, and it will unpack that archive and make sure things are all in order.

Set up from archived KEGG data

anvi-setup-kegg-kofams --kegg-archive KEGG_archive.tar.gz

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.