Power-Efficient Accelerated Genomic Short Read Mapping on Heterogeneous Computing Platforms

Houtgast, E.J.; Sima, V.M.; Marchiori, Giacomo; Bertels, K.L.M.; Al-Ars, Z.

Power-Efficient Accelerated Genomic Short Read Mapping on Heterogeneous Computing Platforms

Abstract (2016)

Authors

E.J. Houtgast Bluebee, Delft, Computer Engineering -

V.M. Sima Computer Engineering - , Bluebee, Delft

Giacomo Marchiori Bluebee, Delft

K.L.M. Bertels Quantum & Computer Engineering , FTQC/Bertels Lab

Z. Al-Ars Computer Engineering -

Research Group

Computer Engineering () (TU Delft)

FPGA Power-efficiency Read mapping

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Published Date

2016

Language

English

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Faculty

Electrical Engineering, Mathematics and Computer Science

Department

Quantum & Computer Engineering

Research Group

Computer Engineering

Abstract

We propose a novel FPGA-accelerated BWA-MEM implementation, a popular tool for genomic data mapping. The performance and power-efficiency of the FPGA implementation on the single Xilinx Virtex-7 Alpha Data add-in card is compared
against a software-only baseline system. By offloading the Seed Extension phase onto the FPGA, a two-fold speedup in overall application-level performance is achieved and a 1.6x gain in power-efficiency. To facilitate platform and tool-agnostic comparisons, the base pairs per Joule unit is introduced as a measure of power-efficiency. The FPGA design is able to map up to 34 thousand base pairs per Joule.