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Simultaneous alignment of short reads against multiple genomes

Schneeberger, Korbinian; Hagmann, Jörg; Ossowski, Stephan; Warthmann, Norman; Gesing, Sandra; Kohlbacher, Oliver; Weigel, Detlef

Description

Genome resequencing with short reads generally relies on alignments against a single reference. GenomeMapper supports simultaneous mapping of short reads against multiple genomes by integrating related genomes (e.g., individuals of the same species) into a single graph structure. It constitutes the first approach for handling multiple references and introduces representations for alignments against complex structures. Demonstrated benefits include access to polymorphisms that cannot be...[Show more]

dc.contributor.authorSchneeberger, Korbinian
dc.contributor.authorHagmann, Jörg
dc.contributor.authorOssowski, Stephan
dc.contributor.authorWarthmann, Norman
dc.contributor.authorGesing, Sandra
dc.contributor.authorKohlbacher, Oliver
dc.contributor.authorWeigel, Detlef
dc.date.accessioned2016-01-11T05:54:20Z
dc.date.available2016-01-11T05:54:20Z
dc.identifier.issn1465-6906
dc.identifier.urihttp://hdl.handle.net/1885/95312
dc.description.abstractGenome resequencing with short reads generally relies on alignments against a single reference. GenomeMapper supports simultaneous mapping of short reads against multiple genomes by integrating related genomes (e.g., individuals of the same species) into a single graph structure. It constitutes the first approach for handling multiple references and introduces representations for alignments against complex structures. Demonstrated benefits include access to polymorphisms that cannot be identified by alignments against the reference alone. Download GenomeMapper at http://1001genomes.org.
dc.description.sponsorshipFinancial support for this work came from a Gottfried Wilhelm Leibniz Award of the Deutsche Forschungsgemeinschaft and the Max Planck Society.
dc.publisherBioMed Central
dc.rightsCopyright © 2009 Schneeberger et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium provided the original work is properly cited.
dc.sourceGenome Biology
dc.subjectalgorithms
dc.subjectbase sequence
dc.subjectcomputational biology
dc.subjectgenome
dc.subjectgenomics
dc.subjectmolecular sequence data
dc.subjectreproducibility of results
dc.subjectsequence alignment
dc.subjectsequence analysis, dna
dc.subjectsequence homology, nucleic acid
dc.subjectsoftware
dc.titleSimultaneous alignment of short reads against multiple genomes
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume10
dc.date.issued2009-09-17
local.identifier.absfor060408
local.identifier.absfor060102
local.identifier.ariespublicationU3488905xPUB1092
local.publisher.urlhttp://www.biomedcentral.com/
local.type.statusPublished Version
local.contributor.affiliationSchneeberger, Korbinian, Max Planck Institute for Developmental Biology, Germany
local.contributor.affiliationHagmann, Jörg, Max Planck Institute for Developmental Biology, Germany
local.contributor.affiliationOssowski, Stephan, Max Planck Institute for Developmental Biology, Germany
local.contributor.affiliationWarthmann, Norman, College of Medicine, Biology and Environment, CMBE Research School of Biology, Division of Plant Sciences, The Australian National University
local.contributor.affiliationGesing, Sandra, Eberhard Karls University , Germany
local.contributor.affiliationKohlbacher, Oliver, Eberhard Karls University, Germany
local.contributor.affiliationWeigel, Detlef, Max Planck Institute for Developmental Biology,, Germany
local.identifier.essn1474-760X
local.bibliographicCitation.issue9
local.bibliographicCitation.startpageR98
local.bibliographicCitation.lastpage12
local.identifier.doi10.1186/gb-2009-10-9-r98
local.identifier.absseo970106
dc.date.updated2016-02-24T09:56:53Z
local.identifier.scopusID2-s2.0-76249113666
local.identifier.thomsonID000271425300019
CollectionsANU Research Publications

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