Microbial 'omics


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anvi-script-filter-hmm-hits-table [program]

Table of Contents

Filter weak HMM hits from a given contigs database using a domain hits table reported by anvi-run-hmms..

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Can provide

hmm-hits

Can consume

contigs-db hmm-source hmm-hits

Usage

This program is for filtering a hmm-source from a hmm-hits in a contigs-db using HMM alignment parameters such as query-coverage and target-coverage. Briefly, the program will remove all records from an hmm-source in the hmm-hits, then import a new hmm-hits table into the contigs-db that was filtered to your specifications.

For this, you first need to ask anvi-run-hmms to ask HMMER to report a domain hits table by including --domain-hits-table flag in your command:

anvi-run-hmms -c contigs-db \ -I Bacteria_71 \ --hmmer-output-dir path/to/DOMTABLE.txt --domain-hits-table

At the end of this run, your HMM hits will be stored in your contigs database as usual. But with the availability of the domain hits table from this run, you can filter out hits from your contigs database using thresholds for query or target coverage of each hit.

For instance following the command above, the command below will remove HMM hits from your contigs database for genes that had less than 90% coverage of the target:

anvi-script-filter-hmm-hits-table -c contigs-db \ --hmm-source Bacteria_71 \ --domain-hits-table path/to/DOMTABLE.txt \ --target-coverage 0.9

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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.