GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference. If you are unsure which one is the appropriate GenomeMapper, you might want to use the latter.

GenomeMapper (for SHORE and WMD3)
Highly accurate short read alignment tool

Short read mapping tool against a single reference.

Project site

GenomeMapper (GraphVersion)
Multiple references alignment

Pre-release of a multiple references alignment tool. Do not use this.

Project site


If you have any questions, don't hesitate to contact us: Korbinian Schneeberger.