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

Quince, C., Delmont, T. O., Raguideau, S., Alneberg, J., Darling, A. E., Collins, G. and Eren, A. M. (2017) DESMAN: a new tool for de novo extraction of strains from metagenomes. Genome Biology, 18, 181. (doi: 10.1186/s13059-017-1309-9) (PMID:28934976) (PMCID:PMC5607848)

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: Articles
• Additional 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.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Collins, Dr Gavin and Quince, Dr Christopher
• Authors: Quince, C., Delmont, T. O., Raguideau, S., Alneberg, J., Darling, A. E., Collins, G., and Eren, A. M.
• College/School: College of Science and Engineering > School of Engineering
• Journal Name: Genome Biology
• Publisher: BioMed Central
• ISSN: 1474-760X
• ISSN (Online): 1465-6906
• Copyright Holders: Copyright © 2017 The Authors
• First Published: First published in Genome Biology 18: 181
• Publisher Policy: Reproduced under a Creative Commons license