anvi-compute-functional-enrichment-across-genomes [program]

A program that computes functional enrichment across groups of genomes..

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Authors

Can consume

groups-txt genomes-storage-db external-genomes internal-genomes functions

Can provide

functional-enrichment-txt

Usage

This program computes functional enrichment across groups of genomes and returns a functional-enrichment-txt file.

For its sister programs, see anvi-compute-functional-enrichment-in-pan and anvi-compute-metabolic-enrichment.

Please also see anvi-display-functions which can both calculate functional enrichment, AND give you an interactive interface to display the distribution of functions.

Functional enrichment

You can use this program by combining genomes described through external-genomes, internal-genomes, and/or stored in a genomes-storage-db. In addition to sources for your genomes, you will need to provide a groups-txt file to declare which genome belongs to which group for enrichment analysis to consider.

How does it work?

1. Aggregate functions from all sources. Gene calls in each genome are tallied according to their functional annotations from the given annotation source.

2. Quantify the distribution of functions in each group of genomes. This information is then used by anvi-script-enrichment-stats to fit a GLM to determine (1) the level that a particular functional annotation is unique to a single group and (2) the percent of genomes it appears in in each group. This produces a functional-enrichment-txt file.

The script anvi-script-enrichment-stats was implemented by Amy Willis, and described first in this paper.

Basic usage

You can use it with a single source of genomes:

or many:

Additional Parameters

You can get a tab-delimited matrix describing the occurrence (counts) of each function within each genome using the --functional-occurrence-table-output parameter:

Edit this file to update this information.

Additional Resources

• A description of the enrichment script run by this program can be found in Shaiber et al 2020

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.