NDLI: Heterogeneous hardware/software acceleration of the BWA-MEM DNA alignment algorithm

Content Provider	IEEE Xplore Digital Library
Author	Ahmed, N. Sima, V.-M. Houtgast, E. Bertels, K. Al-Ars, Z.
Copyright Year	2015
Description	Author affiliation: Comput. Eng. Lab., Delft Univ. of Technol., Delft, Netherlands (Ahmed, N.; Bertels, K.; Al-Ars, Z.) \|\| Bluebee, Delft, Netherlands (Sima, V.-M.; Houtgast, E.)
Abstract	The fast decrease in cost of DNA sequencing has resulted in an enormous growth in available genome data, and hence led to an increasing demand for fast DNA analysis algorithms used for diagnostics of genetic disorders, such as cancer. One of the most computationally intensive steps in the analysis is represented by the DNA read alignment. In this paper, we present an accelerated version of BWA-MEM, one of the most popular read alignment algorithms, by implementing a heterogeneous hardware/software optimized version on the Convey HC2ex platform. A challenging factor of the BWA-MEM algorithm is the fact that it consists of not one, but three computationally intensive kernels: SMEM generation, suffix array lookup and local Smith-Waterman. Obtaining substantial speedup is hence contingent on accelerating all of these three kernels at once. The paper shows an architecture containing two hardware-accelerated kernels and one kernel optimized in software. The two hardware kernels of suffix array lookup and local Smith-Waterman are able to reach speedups of 2.8x and 5.7x, respectively. The software optimization of the SMEM generation kernel is able to achieve a speedup of 1.7x. This enables a total application acceleration of 2.6x compared to the original software version.
Starting Page	240
Ending Page	246
File Size	757169
Page Count	7
File Format	PDF
e-ISBN	9781467383882
DOI	10.1109/ICCAD.2015.7372576
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2015-11-02
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Genomics Bioinformatics DNA Arrays Acceleration Yttrium Software
Content Type	Text
Resource Type	Article

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