| Title: |
Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC |
| Authors: |
Parrello, Bruce; Butler, Rory; Chlenski, Philippe; Pusch, Gordon D.; Overbeek, Ross |
| Contributors: |
Kalendar, Ruslan; National Institute of Allergy and Infectious Diseases |
| Source: |
PLOS ONE ; volume 16, issue 4, page e0250092 ; ISSN 1932-6203 |
| Publisher Information: |
Public Library of Science (PLoS) |
| Publication Year: |
2021 |
| Collection: |
PLOS Publications (via CrossRef) |
| Description: |
Large amounts of metagenomically-derived data are submitted to PATRIC for analysis. In the future, we expect even more jobs submitted to PATRIC will use metagenomic data. One in-demand use case is the extraction of near-complete draft genomes from assembled contigs of metagenomic origin. The PATRIC metagenome binning service utilizes the PATRIC database to furnish a large, diverse set of reference genomes. We provide a new service for supervised extraction and annotation of high-quality, near-complete genomes from metagenomically-derived contigs. Reference genomes are assigned to putative draft genome bins based on the presence of single-copy universal marker roles in the sample, and contigs are sorted into these bins by their similarity to reference genomes in PATRIC. 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. The PATRIC metagenome binning service emphasizes extraction of high-quality genomes for downstream analysis using other PATRIC tools and services. Due to its supervised nature, the binning service is not appropriate for mining novel or extremely low-coverage genomes from metagenomic samples. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| DOI: |
10.1371/journal.pone.0250092 |
| Availability: |
https://doi.org/10.1371/journal.pone.0250092; https://dx.plos.org/10.1371/journal.pone.0250092 |
| Rights: |
https://creativecommons.org/publicdomain/zero/1.0/ |
| Accession Number: |
edsbas.F8FCE33A |
| Database: |
BASE |