Simultaneous alignment of short reads against multiple genomes

Korbinian Schneeberger, Jörg Hagmann, Stephan Ossowski, Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, Detlef Weigel
2009 Genome Biology  
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
more » ... d by alignments against the reference alone. Download GenomeMapper at a Number of known variants in 600 kb of dideoxy sequence data from [38] . b Ratio of confirmed to the sum of confirmed and missed predictions of the respective kind; indicates sensitivity of method. c False discovery rate, percentage of erroneous calls.
doi:10.1186/gb-2009-10-9-r98 pmid:19761611 pmcid:PMC2768987 fatcat:3ewhq2vkafb2ff3uh3deqquphe