MUMmerGPU

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MUMmerGPU is an high-throughput parallel pairwise local sequence alignment program. It uses the GPU to simultaneously align multiple query sequences against a single reference sequence stored as a suffix tree.

Michael Schatz and Cole Trapnell from Center for Bioinformatics and Computation Biology, University of Maryland College Park, contributes the MUMmerGPU implementation to Rodinia

Link: http://mummergpu.sourceforge.net