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

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). ISSN 1474-760X

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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: Article
Additional Information: Funding Information: CQ is funded through a Medical Research Council fellowship (MR/M50161X/1) as part of the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) consortium (MR/L015080/1). GC was supported by a European Research Council Starting Grant (3C-BIOTECH 261330). AME was supported by a Frank R. Lillie Research Innovation Award. Publisher Copyright: © 2017 The Author(s).
Uncontrolled Keywords: metagenomes,niche,strain,ecology, evolution, behavior and systematics,genetics,cell biology ,/dk/atira/pure/subjectarea/asjc/1100/1105
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 08 Sep 2022 15:30
Last Modified: 09 May 2024 10:31
DOI: 10.1186/s13059-017-1309-9

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