Split an anvi'o pan or profile database into smaller, self-contained projects. Black magic..
🔙 To the main page of anvi’o programs and artifacts.
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.
If you ran the following code:
Alternatively you can specify a bin name to limit the reported bins:
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.
Edit this file to update this information.
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.