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

Conference paper (2015)

Authors

E.J. Houtgast Computer Engineering -

V.M. Sima Computer Engineering -

K.L.M. Bertels Computer Engineering -

Z. Al-Ars Computer Engineering -

Research Group

Computer Engineering () (TU Delft)

DOI

https://doi.org/10.1109/SAMOS.2015.7363679

Bioinformatics Acceleration Arrays Genomics Kernel Field programmable gate arrays

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To reference this document use:

http://resolver.tudelft.nl/uuid:eab31b94-0c3d-4315-85a7-3f888f97d70e

Published Date

28-12-2015

Language

English

Reuse Rights

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Faculty

Electrical Engineering, Mathematics and Computer Science

Department

Quantum & Computer Engineering

Research Group

Computer Engineering

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.

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