Split an anvi'o pan or profile database into smaller, self-contained projects. Black magic..
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profile-db contigs-db genomes-storage-db pan-db collection
Creates individual, self-contained anvi’o projects for one or more bins stored in an anvi’o collection. This program may be useful if you would like to share a subset of an anvi’o project with the community or a collaborator, or focus on a particular aspect of your data without having to initialize very large files. Altogether, anvi-split promotoes reproducibility, openness, and collaboration.
The program can generate split-bins from metagenomes or pangenomes. To split bins, you can provide the program anvi-split with a contigs-db and profile-db pair. To split gene clusters, you can provide it with a genomes-storage-db and pan-db pair. In both cases you will also need a collection. If you don’t provide any bin names, the program will create individual directories for each bin that is found in your collection. You can also limit the output to a single bin. Each of the resulting directories in your output folder will contain a stand-alone anvi’o project that can be shared without sharing any of the larger dataset.
Assume you have a profile-db has a collection with three bins, which are (very creatively) called
If you ran the following code:
anvi-split -p profile-db \ -c contigs-db \ -C collection \ -o OUTPUT
Alternatively you can specify a bin name to limit the reported bins:
anvi-split -p profile-db \ -c contigs-db \ -C collection \ --bin-id BIN_1 -o OUTPUT
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.
You can always use the program anvi-show-collections-and-bins to learn available collection and bin names in a given profile-db or pan-db.
For extremely large datasets, splitting bins may be difficult. For metagenomics projets you can,
--skip-variability-tablesto NOT report single-nucleotide variants or single-amino acid variants in your split bins (which can reach hundreds of millions of lines of information for large and complex metagenomes), and/or,
--compress-auxiliary-datato save space. While this is a great option for data that is meant to be stored long-term and shared with the community, the compressed file would need to be manually decompressed by the end-user prior to using the split bin.
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