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

Christopher Quince, Tom O. Delmont, Sébastien Raguideau, Johannes Alneberg, Aaron E. Darling, Gavin Collins, A. Murat Eren

Research output: Contribution to journalArticlepeer-review

84 Citations (Scopus)

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.

Original languageEnglish
Article number181
JournalGenome Biology
Volume18
Issue number1
DOIs
Publication statusPublished - 21 Sep 2017

Keywords

  • Metagenomes
  • Niche
  • Strain

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