Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2021
2021
Historique:
received:
15
12
2020
accepted:
30
03
2021
entrez:
15
4
2021
pubmed:
16
4
2021
medline:
25
9
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 33857229
doi: 10.1371/journal.pone.0250092
pii: PONE-D-20-39369
pmc: PMC8049274
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0250092Subventions
Organisme : NIAID NIH HHS
ID : HHSN272201400027C
Pays : United States
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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