STRONG: Metagenomics strain resolution on assembly graphs

Quince, Christopher, Nurk, Sergey, Raguideau, Sebastien, 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. ISSN 1474-7596

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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: Article
Additional Information: Funding Information: We thank Tatiana Dvorkina (PhD student in SPbSU) for developing the graph-based codon finding algorithm and fruitful discussions. We also acknowledge constructive criticisms from two anonymous reviewers. Andrew Cosgrove was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. The review history is available as Additional file 3. Funding Information: This work for made possible through the MRC Methodology Grant ‘Strain resolved metagenomics for medical microbiology’ MR/S037195/1. CQ is also funded through MRC fellowship (MR/M50161X/1) as part of the CLoud Infrastructure for Microbial Genomics (CLIMB) consortium (MR/L015080/1). SR is funded through BBSRC ‘EBI Metagenomics - enabling the reconstruction of microbial populations’ (BB/R015171/1). OSS acknowledges funding through the BBSRC (BB/N023285/1 and BB/L502029/1). This research was supported in part by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health (SN). Publisher Copyright: © 2021, The Author(s).
Uncontrolled Keywords: assembly graph,bayesian,metagenome,microbial community,microbiome,strains,ecology, evolution, behavior and systematics,genetics,cell biology ,/dk/atira/pure/subjectarea/asjc/1100/1105
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 12 Sep 2022 10:32
Last Modified: 29 Sep 2022 18:31
URI: https://ueaeprints.uea.ac.uk/id/eprint/88109
DOI: 10.1186/s13059-021-02419-7

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