Hardware Acceleration of Short Read Mapping

被引：71

作者：

Olson, Corey B. ^{[1
]}

Kim, Maria ^{[1
]}

Clauson, Cooper ^{[1
]}

Kogon, Boris ^{[1
]}

Ebeling, Carl ^{[1
]}

Hauck, Scott ^{[1
]}

Ruzzo, Walter L. ^{[1
]}

机构：

[1] Univ Washington, Seattle, WA 98195 USA

来源：

2012 IEEE 20TH ANNUAL INTERNATIONAL SYMPOSIUM ON FIELD-PROGRAMMABLE CUSTOM COMPUTING MACHINES (FCCM) | 2012年

关键词：

bioinformatics; short reads; mapping; next-generation sequencing; FPGA; ALIGNMENT;

D O I：

10.1109/FCCM.2012.36

中图分类号：

TP3 [计算技术、计算机技术];

学科分类号：

0812 ;

摘要：

Bioinformatics is an emerging field with seemingly limitless possibilities for advances in numerous areas of research and applications. We propose a scalable FPGA-based solution to the short read mapping problem in DNA sequencing, which greatly accelerates the task of aligning short length reads to a known reference genome. We compare the runtime, power consumption, and sensitivity of the hardware system to the BFAST and Bowtie software tools. The hardware system demonstrates a 250X speedup versus BFAST and a 31X speedup versus Bowtie on eight CPU cores. Also, the hardware system is more sensitive than Bowtie, which aligns approximately 80% of the short reads, as compared to 91% aligned by the hardware.

引用

页码：161 / 168

页数：8

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