Paper Info
Title
Hardware Acceleration of Short Read Mapping
Abstract
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.
Year
DOI
Venue
2012
10.1109/FCCM.2012.36
Field-Programmable Custom Computing Machines
Keywords
Field
DocType
limitless possibility,hardware acceleration,dna sequencing,known reference genome,short length,short read mapping problem,bowtie software tool,power consumption,cpu core,hardware system,numerous area,short read mapping,dna,bioinformatics,genetics,field programmable gate arrays,fpga
Computer science,Parallel computing,Field-programmable gate array,Software,Hardware acceleration,Multi-core processor,Reference genome,Power consumption,Speedup,Scalability
Conference
ISBN
Citations 
PageRank 
978-1-4673-1605-7
53
2.55
References 
Authors
5
7
Name
Order
Citations
PageRank
Corey B. Olson1532.55
Maria Kim2532.55
Cooper Clauson3532.55
Boris Kogon4532.55
Carl Ebeling51405185.32
Scott Hauck62539232.71
Walter L. Ruzzo72727550.25