anvi-script-add-default-collection [program]

A script to add a 'DEFAULT' collection in an anvi'o pan or profile database with a bin named 'EVERYTHING' that describes all items available in the profile database.

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A. Murat Eren (Meren)

Can consume

pan-db profile-db contigs-db

Can provide

collection bin


This program adds a new collection and bin to your pan-db or profile-db and contigs-db pair. This collection and bin will both contain all of your contigs.

This way, you can perform collection and bin specfic operations without having to bin anything yourself. For example, running anvi-interactive in gene-mode requires you to specify a collection and bin (as is done in the Infant Gut Tutorial).

By default, the collection is named DEFAULT and the bin is named EWVERYTHING, but you can change these names with the -C and -b parameters respectively.

Here is an example run on a profile-db:

anvi-script-add-default-collection -c contigs-db \ -p profile-db \ -C MY_COLLECTION \ -b MY_BIN

Once this is run, your profile database will contain a collection called MY_COLLECTION with a single bin (called MY_BIN) which contains all of your contigs.

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.