Publication

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
Eren, A. Murat
Citation
Quince, Christopher; Delmont, Tom O. Raguideau, Sébastien; Alneberg, Johannes; Darling, Aaron E.; Collins, Gavin; Eren, A. Murat (2017). Desman: a new tool for de novo extraction of strains from metagenomes. Genome Biology 18 ,
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.
Funder
Publisher
Springer Nature
Publisher DOI
10.1186/s13059-017-1309-9
Rights
Attribution-NonCommercial-NoDerivs 3.0 Ireland