Paper Info
Title
Acceleration of the long read mapping on a PC-FPGA architecture (abstract only)
Abstract
The genome sequence alignment, whereby ultra scale of sequence reads should be compared to an enormous long reference, has been one central challenge to the biologists for a long period. For recent years, new sequencing technology makes it possible to generate longer reads (sequences of genome fragments) which seem more valuable for the life science research. It has been foreseen that long genome reads (length longer than 200 base pairs) will dominate the field in the near future. Unfortunately, most of the state-of-art aligners nowadays are optimized and only applicable for the short read mapping while present long read aligners are still not satisfying at the aspect of speed. In this paper, we propose a novel PC-FPGA hybrid system to improve the performance of the long read mapping. The BWA-SW algorithm is chosen as the alignment approach and by accelerating the bottleneck of the algorithm, our solution could archive a significant improvement in term of speed. Experiments demonstrate that the described system is as accurate as the BWA-SW aligner and about 1.41-2.73 times faster than it for reads with lengths ranging from 500bp to 2000bp.
Year
DOI
Venue
2013
10.1145/2435264.2435329
FPGA
Keywords
Field
DocType
genome fragment,alignment approach,bwa-sw algorithm,long genome,short read mapping,long read mapping,enormous long reference,bwa-sw aligner,genome sequence alignment,pc-fpga architecture,long period,hardware acceleration,fpga,sequence alignment
Bottleneck,Computer science,Field-programmable gate array,Real-time computing,Ranging,Acceleration,Hardware acceleration,Fpga architecture,Hybrid system
Conference
Citations 
PageRank 
References 
2
0.42
17
Authors
4
Name
Order
Citations
PageRank
Peng Chen1211.89
Chao Wang2352.86
Xi Li320236.61
Xuehai Zhou455177.54