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

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2017-09-21
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Quince, Christopher
 Delmont, Tom O.
 Raguideau, Sébastien
 Alneberg, Johannes
 Darling, Aaron
 Collins, Gavin
 Eren, A. Murat
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https://hdl.handle.net/1912/9292
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https://doi.org/10.1186/s13059-017-1309-9
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10.1186/s13059-017-1309-9
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Keywords
Metagenomes
 Strain
 Niche
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.
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© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology 18 (2017): 181, doi:10.1186/s13059-017-1309-9.
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Genome Biology 18 (2017): 181
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Josephine Bay Paul Center in Comparative Molecular Biology and Evolution
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