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

Chun Yuan Lin, Sheng Ta Li, Che Lun Hung*

*Corresponding author for this work

Research output: Contribution to journalJournal Article peer-review

3 Scopus citations

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.

Original languageEnglish
Pages (from-to)3-10
Number of pages8
JournalInternational Journal of Computational Science and Engineering
Volume9
Issue number1-2
DOIs
StatePublished - 2014

Keywords

  • Approximate string matching
  • CUDA
  • Compute unified device architecture
  • Exact string matching
  • Frequency vector and distance
  • GPUs
  • Graphics processing units
  • Hash look-up table algorithm
  • Next-generation sequencing

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