An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm
Ernst Houtgast (TU Delft - Electrical Engineering, Mathematics and Computer Science)
VM Sima (TU Delft - Electrical Engineering, Mathematics and Computer Science)
K Bertels (TU Delft - Electrical Engineering, Mathematics and Computer Science)
Z Al-Ars (TU Delft - Electrical Engineering, Mathematics and Computer Science)
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Abstract
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.