Metagnome binning is the process of extracting individual genomes from a metagenomic sample. If the sample is in the form of reads, they are assembled into contigs first. Binning contigs involves separating them into sets (called bins) that represent contigs believed to be from a single genome.
This is a supervised binning process: it will only return bins that match genomes in BV-BRC known to be of high quality. You can specify binning of bacterial/archael genomes, virus genomes, or both. All bins will be processed by the Genome Annotation Service to produce annotations and determine the quality of the bin. The resulting genomes will be indexed in the main BV-BRC database as private data and available in searches as well as for use in other BV-BRC services.
This module is a component of the BV-BRC build system. It is designed to fit into the
dev_container infrastructure which manages development and production deployment of
the components of the BV-BRC. More documentation is available here.
The application service specification is given in MetaGenomeBinningthe BV-BRC Comprehensive Genome Annotation service.
The code for the metagenome service itself, along with the code for genome evaluation, is found here.
Aziz, R. K. et al. The RAST Server: rapid annotations using subsystems technology. BMC genomics 9, 75 (2008).
VIGOR4, https://github.com/JCVenterInstitute/VIGOR4.
Parrello B, Butler R, Chlenski P, Olson R, Overbeek J, Pusch G, Vonstein V, Overbeek R. (2019) A machine learning-based service for estimating quality of genomes using PATRIC. BMC Bioinformatics 20, 486 (2019).
Parrello B, Butler R, Chlenski P, Pusch G, Overbeek R. (2021) Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC. PLoS ONE 16(4):e0250092. April 2021