Sciweavers

Share
SAMOS
2015
Springer

An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm

3 years 9 months ago
An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm
—We present the first accelerated implementation of BWA-MEM, a popular genome sequence alignment algorithm widely used in next generation sequencing genomics pipelines. The Smith-Waterman-like sequence alignment kernel requires a significant portion of overall execution time. We propose and evaluate a number of FPGA-based systolic array architectures, presenting optimizations generally applicable to variable length Smith-Waterman execution. Our kernel implementation is up to 3x faster, compared to software-only execution. This translates into an overall application speedup of up to 45%, which is 96% of the theoretically maximum achievable speedup when accelerating only this kernel.
Ernst Joachim Houtgast, Vlad Mihai Sima, Koen Bert
Added 17 Apr 2016
Updated 17 Apr 2016
Type Journal
Year 2015
Where SAMOS
Authors Ernst Joachim Houtgast, Vlad Mihai Sima, Koen Bertels, Zaid Al-Ars
Comments (0)
books