anvi-run-hmms [program]

This program deals with populating tables that store HMM hits in an anvi'o contigs database.

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Can provide


Can consume

contigs-db hmm-source


Stores hmm-hits for a given hmm-source in a contigs-db. In short, this is the program that will do a search for HMMs against a contigs-db and store that information into the contigs-db’s hmm-hits.

This is one of the programs that users commonly run on newly generated contigs-db, along with anvi-scan-trnas, anvi-run-ncbi-cogs, anvi-run-scg-taxonomy, and so on.

What is an HMM?

Check out the lovely vocabulary page for an example here.

Essentially, this program will help annotate the genes in your contigs-db, using either one of the databases built into anvi’o or a custom database.

Basically, in anvi’o, Hidden Markov Models (or HMMs for short) are used to search for specific genes with known functions in a larger dataset. Nucleotide patterns for specific gene functions are contained in an hmm-source and this program uses them to search through the data in your contigs-db.

Default Usage

To run this program with all default settings (against all default anvio hmm-source), you only need to provide a contigs-db.

anvi-run-hmms -c CONTIGS_DB

Running against a custom set of hmm-source

In order to run against your own hmm-source or a custom subset of anvi’o’s hmm-sources, you have two choices.

Choice 1: I have my own hmm-sources on my computer

This way the source can be completely outside of anvi’o.

anvi-run-hmms -c CONTIGS_DB -H path_to_your_hmm_profile

Choice 2: I prefer anvi’o’s hmm-sources, but I don’t need all of them.

By default, anvi’o will look through all of its hmm-sources when doing a search. If you only want to run against a specific one, you’re in the right place. These are the currently available ones: “Bacteria_71” (type: singlecopy), “Archaea_76” (type: singlecopy), “Protista_83” (type: singlecopy), and “Ribosomal_RNAs” (type: Ribosomal_RNAs). See the page for hmm-source for more information.

For example,

anvi-run-hmms -c CONTIGS_DB -I Bacteria_71

Other things anvi-run-hmms can do

  • Add the tag --also-scan-trnas to basically run anvi-scan-trnas for you at the same time. It’s very convientient.
  • Add the tag --just-do-it to hide all warnings and questions in case you don’t want to deal with those.
  • There are also parameters that can help speed up the runtime of this program. However, be aware of the limits of your system, espeically if running on a SGE. For example, you can increase the number of threads or switch to hmmsearch if you are scanning a large umber of HMMs. For more information on that, check out here.

See anvi-run-hmms in action

On the metagenomic workflow tutorial!

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.