SOAP3: Ultra-fast GPU-based parallel alignment tool for short reads

Chi Man Liu, Thomas Wong, Edward Wu, Ruibang Luo, Siu Ming Yiu, Yingrui Li, Bingqiang Wang, Chang Yu, Xiaowen CHU, Kaiyong Zhao, Ruiqiang Li*, Tak Wah Lam

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

176 Citations (Scopus)


SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU. When tested with millions of Illumina Hiseq 2000 length-100 bp reads, SOAP3 takes < 30 s to align a million read pairs onto the human reference genome and is at least 7.5 and 20 times faster than BWA and Bowtie, respectively. For aligning reads with up to four mismatches, SOAP3 aligns slightly more reads than BWA and Bowtie; this is because SOAP3, unlike BWA and Bowtie, is not heuristic-based and always reports all answers.

Original languageEnglish
Article numberbts061
Pages (from-to)878-879
Number of pages2
Issue number6
Publication statusPublished - Mar 2012

Scopus Subject Areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics


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