STRONG: metagenomics strain resolution on assembly graphs

Quince, C; Nurk, S; Raguideau, S; James, R; Soyer, OS; Summers, JK; Limasset, A; Eren, AM; Chikhi, R; Darling, AE

STRONG: metagenomics strain resolution on assembly graphs

Quince, C Nurk, S Raguideau, S James, R Soyer, OS Summers, JK Limasset, A Eren, AM Chikhi, R Darling, AE

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Publisher:: Springer Science and Business Media LLC
Publication Type:: Journal Article
Citation:: Genome Biology, 2021, 22, (1), pp. 214
Issue Date:: 2021-07-26

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Field	Value	Language
dc.contributor.author	Quince, C
dc.contributor.author	Nurk, S
dc.contributor.author	Raguideau, S
dc.contributor.author	James, R
dc.contributor.author	Soyer, OS
dc.contributor.author	Summers, JK
dc.contributor.author	Limasset, A
dc.contributor.author	Eren, AM
dc.contributor.author	Chikhi, R
dc.contributor.author	Darling, AE
dc.date.accessioned	2021-08-27T05:59:23Z
dc.date.available	2021-06-29
dc.date.available	2021-08-27T05:59:23Z
dc.date.issued	2021-07-26
dc.identifier.citation	Genome Biology, 2021, 22, (1), pp. 214
dc.identifier.issn	1474-7596
dc.identifier.issn	1474-760X
dc.identifier.uri	http://hdl.handle.net/10453/150242
dc.description.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.
dc.format	Electronic
dc.language	eng
dc.publisher	Springer Science and Business Media LLC
dc.relation.ispartof	Genome Biology
dc.relation.isbasedon	10.1186/s13059-021-02419-7
dc.rights	info:eu-repo/semantics/openAccess
dc.subject	05 Environmental Sciences, 06 Biological Sciences, 08 Information and Computing Sciences
dc.subject.classification	Bioinformatics
dc.title	STRONG: metagenomics strain resolution on assembly graphs
dc.type	Journal Article
utslib.citation.volume	22
utslib.location.activity	England
utslib.for	05 Environmental Sciences
utslib.for	06 Biological Sciences
utslib.for	08 Information and Computing Sciences
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - ithree - Institute of Infection, Immunity and Innovation
utslib.copyright.status	open_access	*
dc.date.updated	2021-08-27T05:59:17Z
pubs.issue	1
pubs.publication-status	Published
pubs.volume	22
utslib.citation.issue	1

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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http://hdl.handle.net/10453/150242