STRONG: Metagenomics strain resolution on assembly graphs

Christopher Quince, Sergey Nurk, Sebastien Raguideau, Robert James, Orkun S. Soyer, J. Kimberly Summers, Antoine Limasset, A. Murat Eren, Rayan Chikhi, Aaron E. Darling

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)

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.

Original languageEnglish
Article number214
JournalGenome Biology
Volume22
DOIs
Publication statusPublished - 26 Jul 2021

Keywords

  • Assembly graph
  • Bayesian
  • Metagenome
  • Microbial community
  • Microbiome
  • Strains

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