Microbial 'omics


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anvi-import-collection [program]

Table of Contents

Import an external binning result into anvi'o.

🔙 To the main page of anvi’o programs and artifacts.

Authors

A. Murat Eren (Meren)

Can consume

contigs-db profile-db pan-db collection-txt

Can provide

collection

Usage

The purpuse of this program is to import a collection into an anvi’o database.

The input to this program, a collection-txt, may either have been generated by another anvi’o pprogram (such as anvi-export-collection), or may have been generated by the user manually. To import a collection into a database, you can run the following command,

anvi-import-collection collection-txt \ -p profile-db \ -c contigs-db \ -C COLLECTION_NAME

which would import the collection described in the input file formatted as a collection-txt into the profile-db with the name COLLECTION_NAME.

If your collection-txt describes contig names rather than split names, you will likely get an anvi’o error. You can fix that by adding the flag --contigs-mode to your command:

anvi-import-collection collection-txt \ -p profile-db \ -c contigs-db \ --contigs-mode \ -C COLLECTION_NAME

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.