GenomeMapper short read tool published in Genome Biology

Current short read analysis strategies use only a single reference, ignoring previously identified variants.

We have developed a graph mapping approach, that allows simultaneous mapping against all known variants, and thereby greatly increases the number of polymorphisms discovered.Simultaneous alignment of short reads against multiple genomes.

Schneeberger K, Hagmann J, Ossowski S, Warthmann N, Gesing S, Kohlbacher O, Weigel D.

Genome Biol. 2009 Sep 17;10(9):R98. [Epub ahead of print]