Try to check here: https://biomanycores.org

I add a little excerpt from one of our recent papers "Sequence alignment tools: one parallel pattern to rule them all?" (to appear in Hindawi BioMed Research International, cannot add the full paper right now since it is under editorial revision in these days, I'll add to researchgate asap).

Hope it can be useful. Regards.

"An example is SOAP3 [18], the GPU-based version of SOAP2. SOAP3 is at least 7.5 to 20 times faster than BWA and Bowtie, respectively. In addition, BarraCUDA [19] and CUSHAW [20] are short reads alignment tools that exploit GPUs."

[18] C.-M. Liu, T. Wong, E. Wu, R. Luo, S.-M. Yiu, Y. Li, B. Wang, C. Yu, X. Chu, K. Zhao, R. Li, and T.-W. Lam, “Soap3: Ultra-fast gpu-based parallel alignment tool for short reads,” Bioinformatics, vol. 28, no. 6, pp. 878–879, Mar. 2012.

[19] P.Klus,S.Lam,D.Lyberg,M.Cheung,G.Pullan,I.McFarlane,G.Yeo, and B. Lam, “BarraCUDA - a fast short read sequence aligner using graphics processing units,” BMC Research Notes, vol. 5, no. 1, p. 27, 2012.

[20] Y.Liu,B.Schmidt,andD.L.Maskell,“Cushaw:acudacompatibleshort read aligner to large genomes based on the burrows-wheeler transform,” Bioinformatics, 2012.

Maybe take a look also here: http://seqanswers.com/forums/showthread.php?t=30353

Thank you very much, Marco! This is going to be very helpful!!! Best Regards!