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STRONG : metagenomics strain resolution on assembly graphs
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Quince, Christopher , Nurk, Sergey, Raguideau, Sébastien, James, Robert, Soyer, Orkun S., Summers, J. Kimberly, Limasset, Antoine, Eren, A. Murat, Chikhi, Rayan and Darling, Aaron E. (2021) STRONG : metagenomics strain resolution on assembly graphs. Genome Biology, 22 (1). 214. doi:10.1186/s13059-021-02419-7 ISSN 1474-7596.
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WRAP-STRONG-metagenomics-strain-resolution-assembly-graphs-2021.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (4Mb) | Preview |
Official URL: https://doi.org/10.1186/s13059-021-02419-7
Abstract
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.
Item Type: | Journal Article | |||||||||||||||||||||
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Subjects: | Q Science > QR Microbiology | |||||||||||||||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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SWORD Depositor: | Library Publications Router | |||||||||||||||||||||
Library of Congress Subject Headings (LCSH): | Microbial genomics, Microbiology, Microorganisms, Bayesian statistical decision theory -- Graphic methods | |||||||||||||||||||||
Journal or Publication Title: | Genome Biology | |||||||||||||||||||||
Publisher: | BioMed Central Ltd. | |||||||||||||||||||||
ISSN: | 1474-7596 | |||||||||||||||||||||
Official Date: | 26 July 2021 | |||||||||||||||||||||
Dates: |
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Volume: | 22 | |||||||||||||||||||||
Number: | 1 | |||||||||||||||||||||
Article Number: | 214 | |||||||||||||||||||||
DOI: | 10.1186/s13059-021-02419-7 | |||||||||||||||||||||
Status: | Peer Reviewed | |||||||||||||||||||||
Publication Status: | Published | |||||||||||||||||||||
Reuse Statement (publisher, data, author rights): | ** Article version: VoR ** From Crossref journal articles via Jisc Publications Router ** History: epub 26-07-2021; issued 26-07-2021. ** Licence for VoR version of this article starting on 26-07-2021: https://creativecommons.org/licenses/by/4.0 | |||||||||||||||||||||
Access rights to Published version: | Open Access (Creative Commons) | |||||||||||||||||||||
Date of first compliant deposit: | 13 August 2021 | |||||||||||||||||||||
Date of first compliant Open Access: | 16 August 2021 | |||||||||||||||||||||
RIOXX Funder/Project Grant: |
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