@inproceedings{eab31b940c3d431585a73f888f97d70e,
title = "An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm",
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.",
keywords = "Kernel, Arrays, Acceleration, Field programmable gate arrays, Bioinformatics, Genomics",
author = "Ernst Houtgast and VM Sima and K Bertels and Z Al-Ars",
note = "Accepted Author Manuscript; SAMOSXV, Samos, Greege ; Conference date: 19-07-2015 Through 23-07-2015",
year = "2015",
month = dec,
day = "28",
doi = "10.1109/SAMOS.2015.7363679",
language = "English",
isbn = "978-1-4673-7311-1",
publisher = "IEEE",
pages = "221--227",
editor = "D Soudris and L Carro",
booktitle = "Proceedings of the International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation, SAMOS XV",
address = "United States",
}