anvi-split [program]

Split an anvi'o pan or profile database into smaller, self-contained pieces. Provide either a genomes-storage and pan database or a profile and contigs database pair, and you'll get back directories of individual projects for each bin that can be treated as smaller anvi'o projects.

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Can provide

split-bins

Can consume

profile-db contigs-db genomes-storage-db pan-db collection

Usage

This program creates smaller, self-contained anvi’o projects for each of the bins in your project. This is useful if you would like to share a subset of an anvi’o project.

Simply provide either a contigs-db and profile-db pair or a genomes-storage-db and pan-db pair, as well as a collection, and it will create directories for each of your bins that contain their own databases and information. In other words, each of these directories will contain their own anvi’o projects that represent the contigs or genomes stored in that single bin.

An example run

For example, let’s say a profile-db has a collection with three bins, which are (very creatively) called BIN_1, BIN_2, and BIN_3.

If you ran the following code:

Then in the location MY_PATH, you would have three folders: BIN_1, BIN_2, and BIN_3. Each one contains its own profile-db and contigs-db that only contains the contigs from that bin. You can then give a fellow anvi’o user just the BIN_1 directory and they can get to work.

Similarly, if you provide a genomes-storage-db and pan-db pair, the directories will contain their own smaller genomes-storage-db and pan-db pairs.

Other options

You are also able to skip generating variability tables or compress the auxiliary data to save space.

Edit this file to update this information.

Additional Resources

• Anvi-split in action in the pangenomics tutorial

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.