Microbial 'omics


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anvi-compute-completeness [program]

A script to generate completeness info for a given list of splits.

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

Table of Contents

Can provide

Can consume

contigs-db splits-txt hmm-source

Usage

This program tells you the completeness and redundency of single-copy gene sources available for your contigs-db.

For example, some of the defaults are collections of single-copy core genes named Protista_83, Archaea_76, and Bacteria_71. This program will give you a rough estimate of how many Protist, Archaeal, and Bacterial genomes are included in your dataset using these single-copy core genes.

You can use the following run to list available completeness sources in your contigs-db:

anvi-compute-completeness -c contigs-db \ --list-completeness-sources

Then you can run this program on a specifc source as folows:

anvi-compute-completeness -c contigs-db \ --completeness-source Bacteria_71

You can also provide a splits-txt to focus on a specific set of splits, or declare a minimum e-value for a gene to count as a hit. The default is 1e-15.

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.