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Simultaneous alignment of short reads against multiple genomes

Korbinian Schneeberger1, Jörg Hagmann1, Stephan Ossowski1, Norman Warthmann1, Sandra Gesing2, Oliver Kohlbacher2 and Detlef Weigel1*

Author Affiliations

1 Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37-39, D-72076 Tübingen, Germany

2 Center for Bioinformatics Tübingen (ZBIT), Eberhard Karls University Tübingen, Sand 14, 72076 Tübingen, Germany

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Genome Biology 2009, 10:R98  doi:10.1186/gb-2009-10-9-r98

Published: 17 September 2009

Abstract

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 identified by alignments against the reference alone. Download GenomeMapper at http://1001genomes.org webcite.