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Genome Biol. 2009;10(9):R98. doi: 10.1186/gb-2009-10-9-r98. Epub 2009 Sep 17.

Simultaneous alignment of short reads against multiple genomes.

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


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

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