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Extraction of near-complete genomes from metagenomic samples: a new service in PATRIC
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AbstractBackgroundLarge 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.DescriptionThe 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.ConclusionWe provide a new service for rapid and interpretable metagenomic contig binning and annotation in PATRIC.
Cold Spring Harbor Laboratory
Title: Extraction of near-complete genomes from metagenomic samples: a new service in PATRIC
Description:
AbstractBackgroundLarge 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.
DescriptionThe 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.
ConclusionWe provide a new service for rapid and interpretable metagenomic contig binning and annotation in PATRIC.
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