anvi-script-gen-function-matrix-across-genomes

A program to generate reports for the distribution of functions across genomes.

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Authors

Can consume

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

Can provide

functional-enrichment-txt functions-across-genomes-txt

Usage

Generates TAB-delmited output files for functions from a single function annotation source across genomes.

For a simlar program that reports HMM hits across genomes, see anvi-script-gen-hmm-hits-matrix-across-genomes.

The input genomes for this program can be provided through an external-genomes, internal-genomes, genomes-storage-db, or any combination of these sources.

This program is very similar to anvi-display-functions, and can also perform a functional enrichment analysis on-the-fly if you provide it with an optional groups-txt file. Unlike, anvi-display-functions, this program will report TAB-delmited output files for you to further analyze.

You can run the program on a set of genomes for a given annotation source:

The command above will result in two files in your work directory, both of which will be of type functions-across-genomes-txt:

• MY-GENOMES-FREQUENCY.txt
• MY-GENOMES-PRESENCE-ABSENCE.txt

You can always learn about which functions are in a given contigs-db using the program anvi-db-info.

Alternatively you can run it with a groups-txt that associates sets of genomes with distinct groups,

which would generate an additional file in your work directory of type functional-enrichment-txt:

• MY-GENOMES-FUNCTIONAL-ENRICHMENT.txt

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.