PSAEC: an improved algorithm for short read error correction using partial suffix arrays

Authors:
Zhiheng Zhao;Jianping Yin;Yubin Zhan;Wei Xiong;Yong Li;Fayao Liu
Affiliations:
School of Computer, National University of Defense Technology, Changsha, China;School of Computer, National University of Defense Technology, Changsha, China;School of Computer, National University of Defense Technology, Changsha, China;School of Computer, National University of Defense Technology, Changsha, China;School of Computer, National University of Defense Technology, Changsha, China;School of Computer, National University of Defense Technology, Changsha, China
Venue:
FAW-AAIM'11 Proceedings of the 5th joint international frontiers in algorithmics, and 7th international conference on Algorithmic aspects in information and management
Year:
2011

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ACM Computing Surveys (CSUR)
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Abstract

Sequencing errors in high-throughput sequencing data constitute one of the major problems in analyzing such data. Error correction can reduce the error rate. However, it is a computation and data intensive process for large-scale data. This poses challenges for more efficient and scalable algorithms. In this paper, we propose PSAEC, an improved algorithm for short read error correction using partial suffix arrays in high-throughput sequencing data. Our algorithm optimizes the HiTEC program by replacing full suffix arrays with partial suffix arrays to index reads which is more time and space efficient. Moreover, PSAEC is a scalable parallel algorithm that can works well on multi-core computers using Pthread. Experiments show that our algorithm delivers good, scalable performance.