STRONG: metagenomics strain resolution on assembly graphs.
Assembly graph
Bayesian
Metagenome
Microbial community
Microbiome
Strains
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
26 07 2021
26 07 2021
Historique:
received:
22
08
2020
accepted:
29
06
2021
entrez:
27
7
2021
pubmed:
28
7
2021
medline:
22
1
2022
Statut:
epublish
Résumé
We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads.
Identifiants
pubmed: 34311761
doi: 10.1186/s13059-021-02419-7
pii: 10.1186/s13059-021-02419-7
pmc: PMC8311964
doi:
Types de publication
Journal Article
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
214Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/R015171/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/M50161X/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/N023285/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/S037195/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/K003240/2
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/L015080/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/L502029/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BBS/E/T/000PR9817
Pays : United Kingdom
Informations de copyright
© 2021. The Author(s).
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