anvi-run-cazymes
Table of Contents
Run dbCAN CAZymes on contigs-db.
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Usage
This program annotates genes in your contigs-db with functions using dbCAN CAZyme HMMs
Before you run this program, you’ll have to set up the CAZyme database on your computer with the program anvi-setup-cazymes.
The CAZyme database is based on protein sequences, so anvi’o will convert your genetic information into protein sequences and then use HMMs to compare them to the database.
Unsure what an HMM is? Check out our vocab page
To run, you’ll need to provide a contigs-db and the output will be a functions artifact. Here is a default run:
anvi-run-cazymes -c contigs-db
If you stored the cazyme-data that you got from running anvi-setup-cazymes in a custom location, you’ll need to provide that path as well.
anvi-run-cazymes -c contigs-db \ --cazyme-data-dir cazyme-data
By default, this uses hmmsearch to run HMMs. You can choose to use hmmscan instead by running
anvi-run-cazymes -c contigs-db \ --cazyme-data-dir cazyme-data \ --hmmer-program hmmscan
Use the parameter --noise-cutoff-terms to filter out hits. The default value is --noise-cutoff-terms -E 1e-12. If you want to explore filtering options, check out the help menu of the underlying hmm program you are using e.g. hmmsearch -h
anvi-run-cazymes -c contigs-db \ --noise-cutoff-terms “-E 1e-14”
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.