anvi-compute-completeness

Authors
Requires
Can use
Provides
Usage
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

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

🔙 To the main page of anvi’o programs and artifacts.

Authors

A. Murat Eren (Meren)

Requires

contigs-db

Can use

splits-txt hmm-source

Provides

This program does not seem to provide any artifacts. Such programs usually print out some information for you to see or alter some anvi’o artifacts without producing any immediate outputs.

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.

Command line interface

The following is the list of parameters and their descriptions in the latest version of anvi-compute-completeness.

The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).

Command line usage

anvi-compute-completeness [-h] [--splits-of-interest FILE] -c CONTIGS_DB [-e E-VALUE] [--list-completeness-sources] [--completeness-source NAME]

Parameters and their descriptions

options

--splits-of-interest FILE: A file with split names. There should be only one column in the file, and each line should correspond to a unique split name.
-c, --contigs-db CONTIGS_DB required: Anvi'o contigs database generated by 'anvi-gen-contigs-database'
-e, --min-e-value E-VALUE: Minimum significance score of an HMM find to be considered as a valid hit. Default is 1e-15. Default: 0.000000000000001
--list-completeness-sources: Show available sources and exit.
--completeness-source NAME: Single-copy gene source to use to estimate completeness.

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.