anvi-import-contig-classification

Import contig-level classification data (domain, virus, plasmid, etc.) into a contigs database from a user-prepared tab-delimited file.

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Authors

Requires

contigs-db contig-classification-txt

Provides

contig-classification

Usage

This program takes in one or more contig-classification-txt files and stores the contig-level classification data in a contigs-db, producing a contig-classification artifact.

There are many software tools available for classifying contigs according to their predicted domain of origin, and the point of this program is to put those classifications within a contigs-db for use in downstream programs such as anvi-split. In order for this to work, you’ll need to convert the output of whichever tool you have used to the standardized tabular format accepted by this program. Once you have a contig-classification-txt containing the classification data, you can import that data like this:

Multiple classification sources can coexist in the same contigs database, as described by the source column in the input file. If you want to import multiple sources, you can put all their classifications into one contig-classification-txt.

That said, in case you created a different table for each classification tool that you used, you can import from multiple files at once:

If your input file contains classifications from a source that is already stored in the contigs database, anvi’o will raise an error to protect existing data. To overwrite a source, re-run with the --just-do-it flag, which will delete all existing rows for that source before inserting the new data:

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.