Microbial 'omics

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anvi-export-collection [program]

Export a collection from an anvi'o database.

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

Table of Contents



Requires or uses

profile-db collection


This program, as one might think, allows you to export a collection. This allows you to take your binning results elsewhere (including into another Anvi’o project with the command anvi-import-collection).

You can run this program on a profile-db or pan-db as follows:

anvi-export-collection -C my_favorite_collection \ -p profile-db

This will give you a collection-txt file that describes the collection my_favorite_collection.

To list the collections available in this database, you can run

anvi-export-collection -p pan-db \ --list-colllections

You can also add the flag --include-unbinned to have all unbinned contigs in the database show up at the end of your collection-txt file in a bin titled UNBINNED.

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.