anvi-script-add-default-collection

A script to add a 'DEFAULT' collection in an anvi'o pan or profile database with either (1) a single bin that describes all items available in the profile database, or (2) as many bins as there are items in the profile database wher every item has its own bin. The former is the default behavior that will be useful in most instances where you need to use this script. The latter is most useful if you are Florian and/or have something very specific in mind..

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Authors

Can consume

pan-db profile-db contigs-db

Can provide

collection bin

Usage

This program adds a ‘default’ collection and bin to your pan-db or profile-db and contigs-db that describes every item in your database.

This way, you can perform anvi’o tasks that require a collection or a bin even if you do not have a particular collection for your data, or all items in your database represent a meaningful bin (such as every contig in a contigs-db that represents a single genome).

As an example, see this program in action in the Infant Gut Tutorial where it is used to run anvi-interactive on a genome in ‘gene mode’.

Run in its simples form,

the program will add a new collection into the profile database named DEFAULT, which will contain a single bin that describes all items in the database named EVERYTHING. You can set these default names to your liking using additional parameters:

Also see related programs, anvi-show-collections-and-bins and anvi-delete-collection.

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.