Extraction of near-complete genomes from metagenomic samples: a new service in PATRIC

Background Large volumes of metagenomic samples are being processed and submitted to PATRIC for analysis as reads or assembled contigs. Effective analysis of these samples requires solutions to a number of problems, including the binning of assembled, mixed, metagenomically-derived contigs into taxonomic units. Description The PATRIC metagenome binning service utilizes the PATRIC database to furnish a large, diverse set of reference genomes. Reference genomes are assigned based on the presence of single-copy universal marker proteins in the sample, and contigs are assigned to the bin corresponding to the most similar reference genome. Each set of binned contigs represents a draft genome that will be annotated by RASTtk in PATRIC. A structured-language binning report is provided containing quality measurements and taxonomic information about the contig bins. Conclusion We provide a new service for rapid and interpretable metagenomic contig binning and annotation in PATRIC.