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

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....

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Autores principales: Quince, Christopher, Delmont, Tom O., Raguideau, Sébastien, Alneberg, Johannes, Darling, Aaron E., Collins, Gavin, Eren, A. Murat
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607848/
https://www.ncbi.nlm.nih.gov/pubmed/28934976
http://dx.doi.org/10.1186/s13059-017-1309-9
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author Quince, Christopher
Delmont, Tom O.
Raguideau, Sébastien
Alneberg, Johannes
Darling, Aaron E.
Collins, Gavin
Eren, A. Murat
author_facet Quince, Christopher
Delmont, Tom O.
Raguideau, Sébastien
Alneberg, Johannes
Darling, Aaron E.
Collins, Gavin
Eren, A. Murat
author_sort Quince, Christopher
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-017-1309-9) contains supplementary material, which is available to authorized users.
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spelling pubmed-56078482017-09-24 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 Genome Biol Method 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-017-1309-9) contains supplementary material, which is available to authorized users. BioMed Central 2017-09-21 /pmc/articles/PMC5607848/ /pubmed/28934976 http://dx.doi.org/10.1186/s13059-017-1309-9 Text en © The Author(s) 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Quince, Christopher
Delmont, Tom O.
Raguideau, Sébastien
Alneberg, Johannes
Darling, Aaron E.
Collins, Gavin
Eren, A. Murat
DESMAN: a new tool for de novo extraction of strains from metagenomes
title DESMAN: a new tool for de novo extraction of strains from metagenomes
title_full DESMAN: a new tool for de novo extraction of strains from metagenomes
title_fullStr DESMAN: a new tool for de novo extraction of strains from metagenomes
title_full_unstemmed DESMAN: a new tool for de novo extraction of strains from metagenomes
title_short DESMAN: a new tool for de novo extraction of strains from metagenomes
title_sort desman: a new tool for de novo extraction of strains from metagenomes
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607848/
https://www.ncbi.nlm.nih.gov/pubmed/28934976
http://dx.doi.org/10.1186/s13059-017-1309-9
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