Microbial 'omics

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anvi-script-gen-genomes-file [program]

Generate an external genomes or internal genomes file.

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

Table of Contents

Can provide

external-genomes internal-genomes

Can consume

contigs-db profile-db collection


This script can automatically generate an external or internal genomes file.

Generating an external genomes file

If you provide an input directory and a name for the output file, then every contigs-db in that directory will get a line in the resulting external-genomes file:

anvi-script-gen-genomes-file --input-dir path/to/dir -e external_genomes.txt

The name of each database will be whatever string is in front of the *.db extension, and the contigs_db_path column will contain absolute paths.

Generating an internal genomes file

To get an internal-genomes file containing all bins from a collection, provide a profile-db, its corresponding contigs-db, and the collection name:

anvi-script-gen-genomes-file -i internal_genomes.txt -c CONTIGS.db -p PROFILE.db -C default

The name of each internal genome will be the same as the bin name, and the path columns will contain absolute paths.

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.