NDLI: Reconfigurable Acceleration of Short Read Mapping

Content Provider	IEEE Xplore Digital Library
Author	Arram, J. Kuen Hung Tsoi Luk, W. Peiyong Jiang
Copyright Year	2013
Description	Author affiliation: Dept. of Comput., Imperial Coll. London, London, UK (Arram, J.; Kuen Hung Tsoi; Luk, W.) \|\| Dept. of Chem. Pathology, Chinese Univ. of Hong Kong, Hong Kong, China (Peiyong Jiang)
Abstract	Recent improvements in the throughput of nextgeneration DNA sequencing machines poses a great computational challenge in analysing the massive quantities of data produced. This paper proposes a novel approach, based on reconfigurable computing technology, for accelerating short read mapping, where the positions of millions of short reads are located relative to a known reference sequence. Our approach consists of two key components: an exact string matcher for the bulk of the alignment process, and an approximate string matcher for the remaining cases. We characterise interesting regions of the design space, including homogeneous, heterogeneous and run-time reconfigurable designs and provide back of envelope estimations of the corresponding performance. We show that a particular implementation of this architecture targeting a single FPGA can be up to 293 times faster than BWA on an Intel X5650 CPU, and 134 times faster than SOAP3 on an NVIDIA GTX 580 GPU.
Sponsorship	IEEE Comput. Soc.
Starting Page	210
Ending Page	217
File Size	386472
Page Count	8
File Format	PDF
ISBN	9781467360050
e-ISBN	9780769549699
DOI	10.1109/FCCM.2013.57
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2013-04-28
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Field programmable gate arrays Arrays Hardware DNA Sociology Statistics
Content Type	Text
Resource Type	Article

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