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Open Access Methodology article

HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data

Adrianto Wirawan1*, Robert S Harris2, Yongchao Liu1, Bertil Schmidt1* and Jan Schröder34

Author Affiliations

1 Institut für Informatik, Johannes Gutenberg Universität Mainz, Mainz, Germany

2 Department of Biology, The Pennsylvania State University, University Park, State College, Pennsylvania, PA 16801, USA

3 Bioinformatics Division, Walter and Eliza Hall Institute, Melbourne, Australia

4 Department of Molecular Medicine, The University of Melbourne, Melbourne, Australia

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BMC Bioinformatics 2014, 15:131  doi:10.1186/1471-2105-15-131

Published: 6 May 2014

Abstract

Background

Current-generation sequencing technologies are able to produce low-cost, high-throughput reads. However, the produced reads are imperfect and may contain various sequencing errors. Although many error correction methods have been developed in recent years, none explicitly targets homopolymer-length errors in the 454 sequencing reads.

Results

We present HECTOR, a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. In this algorithm, for the first time we have investigated a novel homopolymer spectrum based approach to handle homopolymer insertions or deletions, which are the dominant sequencing errors in 454 pyrosequencing reads. We have evaluated the performance of HECTOR, in terms of correction quality, runtime and parallel scalability, using both simulated and real pyrosequencing datasets. This performance has been further compared to that of Coral, a state-of-the-art error corrector which is based on multiple sequence alignment and Acacia, a recently published error corrector for amplicon pyrosequences. Our evaluations reveal that HECTOR demonstrates comparable correction quality to Coral, but runs 3.7× faster on average. In addition, HECTOR performs well even when the coverage of the dataset is low.

Conclusion

Our homopolymer spectrum based approach is theoretically capable of processing arbitrary-length homopolymer-length errors, with a linear time complexity. HECTOR employs a multi-threaded design based on a master-slave computing model. Our experimental results show that HECTOR is a practical 454 pyrosequencing read error corrector which is competitive in terms of both correction quality and speed. The source code and all simulated data are available at: http://hector454.sourceforge.net webcite.

Keywords:
NGS error correction; Homopolymer-length error; 454 sequencing; Parallelization