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

doi:10.1186/s13059-021-02419-7

STRONG: metagenomics strain resolution on assembly graphs

Genome Biol. 2021 Jul 26;22(1):214. doi: 10.1186/s13059-021-02419-7.

Authors

Christopher Quince^{1

2

3}, Sergey Nurk⁴, Sebastien Raguideau^{5

6}, Robert James⁷, Orkun S Soyer⁸, J Kimberly Summers⁶, Antoine Limasset⁹, A Murat Eren^{10

11}, Rayan Chikhi¹², Aaron E Darling¹³

Affiliations

¹ Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK. christopher.quince@earlham.ac.uk.
² Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK. christopher.quince@earlham.ac.uk.
³ Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK. christopher.quince@earlham.ac.uk.
⁴ Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892, MD, USA. sergey.nurk@nih.gov.
⁵ Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK.
⁶ Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
⁷ Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK.
⁸ School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
⁹ Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL, Lille, France.
¹⁰ Department of Medicine, University of Chicago, Chicago, Illinois, USA.
¹¹ Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA.
¹² Department of Computational Biology, Institut Pasteur, C3BI USR 3756 IP CNRS, Paris, France.
¹³ The iThree institute, University of Technology Sydney, 15 Broadway, Ultimo, 2007, NSW, Australia.

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.

Keywords: Assembly graph; Bayesian; Metagenome; Microbial community; Microbiome; Strains.

Publication types

Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Bayes Theorem
Contig Mapping
Genome, Bacterial*
Haplotypes
Metagenome*
Metagenomics / methods
Microbial Consortia / genetics*
Sequence Analysis, DNA
Software*

Abstract

Publication types

MeSH terms

Grants and funding