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DESMAN : a new tool for de novo extraction of strains from metagenomes

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Quince, Christopher , Delmont, Tom O., Raguideau, Sébastien, Alneberg, Johannes, Darling, Aaron E., Collins, Gavin and Eren, A. Murat (2017) DESMAN : a new tool for de novo extraction of strains from metagenomes. Genome Biology, 18 (1). doi:10.1186/s13059-017-1309-9

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Official URL: http://dx.doi.org/10.1186/s13059-017-1309-9

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Abstract

We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain. We validated DESMAN on a complex 50-species 210-genome 96-sample synthetic mock data set and then applied it to the Tara Oceans microbiome.

Item Type: Journal Article
Divisions: Faculty of Medicine > Warwick Medical School > Biomedical Sciences
Faculty of Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection
Faculty of Medicine > Warwick Medical School
Journal or Publication Title: Genome Biology
Publisher: BioMed Central Ltd.
ISSN: 1474-7596
Official Date: 21 September 2017
Dates:
DateEvent
21 September 2017Published
25 August 2017Accepted
Volume: 18
Number: 1
DOI: 10.1186/s13059-017-1309-9
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
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