Acceleration of the long read mapping on a PC-FPGA architecture (abstract only)

Authors:
Peng Chen;Chao Wang;Xi Li;Xuehai Zhou
Affiliations:
University of Sciense and Technology of China, HeFei, China;University of Sciense and Technology of China, HeFei, China;University of Sciense and Technology of China, HeFei, China;University of Sciense and Technology of China, HeFei, China
Venue:
Proceedings of the ACM/SIGDA international symposium on Field programmable gate arrays
Year:
2013

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Abstract

The genome sequence alignment, whereby ultra scale of sequence reads should be compared to an enormous long reference, has been one central challenge to the biologists for a long period. For recent years, new sequencing technology makes it possible to generate longer reads (sequences of genome fragments) which seem more valuable for the life science research. It has been foreseen that long genome reads (length longer than 200 base pairs) will dominate the field in the near future. Unfortunately, most of the state-of-art aligners nowadays are optimized and only applicable for the short read mapping while present long read aligners are still not satisfying at the aspect of speed. In this paper, we propose a novel PC-FPGA hybrid system to improve the performance of the long read mapping. The BWA-SW algorithm is chosen as the alignment approach and by accelerating the bottleneck of the algorithm, our solution could archive a significant improvement in term of speed. Experiments demonstrate that the described system is as accurate as the BWA-SW aligner and about 1.41-2.73 times faster than it for reads with lengths ranging from 500bp to 2000bp.