Title: Frequency-based re-sequencing tool for short reads on graphics processing units

Authors: Chun-Yuan Lin; Sheng-Ta Li; Che Lun Hung

Addresses: Department of Computer Science and Information Engineering, Chang Gung University, Tao-Yuan 333, Taiwan ' Department of Computer Science and Information Engineering, Chang Gung University, Tao-Yuan 333, Taiwan ' Department of Computer Science and Communication Engineering, Providence University, Taichung 433, Taiwan

Abstract: After the reference genomes of many organisms are sequenced in the post-genetic era, an important issue is to do the re-sequencing of individual genomes with high-throughput reads. Many next-generation sequencing machines have been proposed in the last few years and a series of re-sequencing tools have been developed for mapping short reads to the reference genome. FRESCO is a frequency-based re-sequencing tool without using hash look-up table algorithm and Burrows-Wheeler transformation. FRESCO offers more flexibility in the mapping and then obtains satisfactory mapping results. However, FRESCO is a computation-intensive tool. Therefore, in this paper, a tool, CUDA-FRESCO v1.0, was proposed to reduce the computation time of FRESCO by using the graphics processing units with CUDA. By comparing to FRESCO, CUDA-FRESCO v1.0 achieved 63× speedups for the mapping kernel and 20× speedups for the overall computation time.

Keywords: gene sequencing; next-generation sequencing; exact string matching; approximate string matching; compute unified device architecture; CUDA; graphics processing units; GPUs; hash look-up table algorithm; frequency vector; distance; bioinformatics.

DOI: 10.1504/IJCSE.2014.058686

International Journal of Computational Science and Engineering, 2014 Vol.9 No.1/2, pp.3 - 10

Received: 17 Feb 2012
Accepted: 08 Mar 2012
Published online: 24 May 2014 *

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