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Journal Articles Genome Biology Year : 2021

STRONG: metagenomics strain resolution on assembly graphs

Christopher Quince
Sergey Nurk
  • Function : Author
Sebastien Raguideau
  • Function : Author
Robert James
  • Function : Author
Orkun Soyer
  • Function : Author
J. Kimberly Summers
  • Function : Author
A. Murat Eren
  • Function : Author
Rayan Chikhi
Aaron Darling

Abstract

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.
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Dates and versions

hal-03443171 , version 1 (25-11-2022)

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Antoine Limasset, Christopher Quince, Sergey Nurk, Sebastien Raguideau, Robert James, et al.. STRONG: metagenomics strain resolution on assembly graphs. Genome Biology, 2021, 22 (1), ⟨10.1186/s13059-021-02419-7⟩. ⟨hal-03443171⟩
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