DESMAN : a new tool for de novo extraction of strains from metagenomes
DESMAN : a new tool for de novo extraction of strains from metagenomes
| dc.contributor.author | Quince, Christopher | |
| dc.contributor.author | Delmont, Tom O. | |
| dc.contributor.author | Raguideau, Sébastien | |
| dc.contributor.author | Alneberg, Johannes | |
| dc.contributor.author | Darling, Aaron | |
| dc.contributor.author | Collins, Gavin | |
| dc.contributor.author | Eren, A. Murat | |
| dc.date.accessioned | 2017-10-10T19:45:06Z | |
| dc.date.available | 2017-10-10T19:45:06Z | |
| dc.date.issued | 2017-09-21 | |
| dc.description | © 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. | en_US |
| dc.description.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. | en_US |
| dc.description.sponsorship | 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. | en_US |
| dc.identifier.citation | Genome Biology 18 (2017): 181 | en_US |
| dc.identifier.doi | 10.1186/s13059-017-1309-9 | |
| dc.identifier.uri | https://hdl.handle.net/1912/9292 | |
| dc.language.iso | en_US | en_US |
| dc.publisher | BioMed Central | en_US |
| dc.relation.uri | https://doi.org/10.1186/s13059-017-1309-9 | |
| dc.rights | Attribution 4.0 International | * |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | * |
| dc.subject | Metagenomes | en_US |
| dc.subject | Strain | en_US |
| dc.subject | Niche | en_US |
| dc.title | DESMAN : a new tool for de novo extraction of strains from metagenomes | en_US |
| dc.type | Article | en_US |
| dspace.entity.type | Publication | |
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