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2015 IEEE 23rd Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM) (2015)
Vancouver, BC, Canada
May 2, 2015 to May 6, 2015
ISBN: 978-1-4799-9969-9
pp: 199-202
ABSTRACT
The Smith-Waterman (S-W) algorithm is widely adopted by the state-of-the-art DNA sequence aligners. Existing wave front-based methods ignored the fact that the S-W algorithm is fed with significantly varied-size inputs in modern aligners, in which the S-W algorithm is further optimized by exerting extensive pruning. In this paper, we propose an architecture, tailored for varied input sizes as well as harnessing software pruning strategies, to accelerate S-W. Our implementation demonstrates a 26.4x speedup over a 24-thread Intel Has well Xeon server, and outperforms wave front-based implementations by up to 6x with the same FPGA resource.
INDEX TERMS
Field programmable gate arrays, Parallel processing, Algorithm design and analysis, Computer architecture, Bioinformatics, Kernel
CITATION

Y. Chen, J. Cong, J. Lei and P. Wei, "A Novel High-Throughput Acceleration Engine for Read Alignment," 2015 IEEE 23rd Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM), Vancouver, BC, Canada, 2015, pp. 199-202.
doi:10.1109/FCCM.2015.27
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