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

Quince, C; Delmont, TO; Raguideau, S; Alneberg, J; Darling, AE; Collins, G; Eren, AM

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

Quince, C Delmont, TO Raguideau, S Alneberg, J Darling, AE

Collins, G Eren, AM

Permalink

Publication Type:: Journal Article
Citation:: Genome Biology, 2017, 18 (1)
Issue Date:: 2017-09-21

Open Access

Copyright Clearance Process

Recently Added
In Progress
Open Access

This item is open access.

Adobe PDF

Download Accepted Manuscript VersionAdobe PDF (2.41 MB)

View on publisher's site

View statistics

Full metadata record

Field	Value	Language
dc.contributor.author	Quince, C	en_US
dc.contributor.author	Delmont, TO	en_US
dc.contributor.author	Raguideau, S	en_US
dc.contributor.author	Alneberg, J	en_US
dc.contributor.author	Darling, AE https://orcid.org/0000-0003-2397-7925	en_US
dc.contributor.author	Collins, G	en_US
dc.contributor.author	Eren, AM	en_US
dc.date.available	2017-08-25	en_US
dc.date.issued	2017-09-21	en_US
dc.identifier.citation	Genome Biology, 2017, 18 (1)	en_US
dc.identifier.issn	1474-7596	en_US
dc.identifier.uri	http://hdl.handle.net/10453/121937
dc.description.abstract	© 2017 The Author(s). 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.relation	http://purl.org/au-research/grants/arc/LP150100912
dc.relation.ispartof	Genome Biology	en_US
dc.relation.isbasedon	10.1186/s13059-017-1309-9	en_US
dc.subject.classification	Bioinformatics	en_US
dc.subject.mesh	Sequence Analysis, DNA	en_US
dc.subject.mesh	Haplotypes	en_US
dc.subject.mesh	Polymorphism, Genetic	en_US
dc.subject.mesh	Genome, Bacterial	en_US
dc.subject.mesh	Software	en_US
dc.subject.mesh	Metagenome	en_US
dc.subject.mesh	Microbiota	en_US
dc.title	DESMAN: A new tool for de novo extraction of strains from metagenomes	en_US
dc.type	Journal Article
utslib.citation.volume	1	en_US
utslib.citation.volume	18	en_US
utslib.for	0599 Other Environmental Sciences	en_US
utslib.for	0604 Genetics	en_US
utslib.for	0803 Computer Software	en_US
utslib.for	05 Environmental Sciences	en_US
utslib.for	06 Biological Sciences	en_US
utslib.for	08 Information and Computing Sciences	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - ithree - Institute of Infection, Immunity and Innovation
utslib.copyright.status	open_access
pubs.issue	1	en_US
pubs.publication-status	Published	en_US
pubs.volume	18	en_US

Abstract:

© 2017 The Author(s). 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.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/121937