Microbial 'omics


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anvi-import-collection [program]

Import an external binning result into anvi'o.

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

Table of Contents

Provides

collection

Requires or uses

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

Usage

This program, as one might think, allows you to import a collection. This allows you to easily import any binning that you’ve already done into a profile-db, since the bins within that collection will be carried over.

This information (in the form of a collection-txt) can either come from another Anvi’o project (using anvi-export-collection) or you can get the coverage and sequence composion of your data using anvi-export-splits-and-coverages to bin your contigs with software outside of Anvi’o, then import that data into your database with this program.

You can run this program like so:

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

This will import the collection indicated in my_bins.txt into your profile-db.

my_bins.txt should be a tab-delimited file where the first column lists a split name and the second lists the bin that it is placed in. You can see an example of this here.

You can also provide this information by listing your contigs instead of your splits (like this). Just add the --contigs-mode tag.

You can also provide an information file to describe the source and/or colors of your bins. This file is an example of such an information file.

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.