HECTOR: A parallel multistage homopolymer spectrum based error corrector for 454 sequencing data
Adrianto Wirawan, Robert S. Harris, Yongchao Liu, Bertil Schmidt, Jan Schröder
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.
BMC bioinformatics
https://doi.org/10.1186/1471-2105-15-131
Dive into the research topics of 'HECTOR: A parallel multistage homopolymer spectrum based error corrector for 454 sequencing data'. Together they form a unique fingerprint.
Homopolymerization Engineering & Materials Science 100%
Corrector Mathematics 80%
Sequencing Mathematics 80%
Anthozoa Medicine & Life Sciences 63%
Single Monomer Polymer Chemical Compounds 63%
Wirawan, A., Harris, R. S., Liu, Y., Schmidt, B., & Schröder, J. (2014). HECTOR: A parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. BMC bioinformatics, 15(1), [131]. https://doi.org/10.1186/1471-2105-15-131
Wirawan, Adrianto ; Harris, Robert S. ; Liu, Yongchao et al. / HECTOR : A parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. In: BMC bioinformatics. 2014 ; Vol. 15, No. 1.
@article{a162bfe743894db9bfc967d9a14a8fd8,
title = "HECTOR: A parallel multistage homopolymer spectrum based error corrector for 454 sequencing data",
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.",
author = "Adrianto Wirawan and Harris, {Robert S.} and Yongchao Liu and Bertil Schmidt and Jan Schr{\"o}der",
note = "Funding Information: The authors thank the editor and the anonymous reviewers for their helpful and constructive comments which helped to improve the manuscript. JS received salary support from National Health and Medical Research Council (NHMRC) Program Grant (1054618). The research benefitted by the support from the Victorian State Government Operational Infrastructure Support and Australian Government NHMRC IRIISS.",
doi = "10.1186/1471-2105-15-131",
journal = "BMC Bioinformatics",
Wirawan, A, Harris, RS, Liu, Y, Schmidt, B & Schröder, J 2014, 'HECTOR: A parallel multistage homopolymer spectrum based error corrector for 454 sequencing data', BMC bioinformatics, vol. 15, no. 1, 131. https://doi.org/10.1186/1471-2105-15-131
HECTOR : A parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. / Wirawan, Adrianto; Harris, Robert S.; Liu, Yongchao et al.
In: BMC bioinformatics, Vol. 15, No. 1, 131, 06.05.2014.
T1 - HECTOR
T2 - A parallel multistage homopolymer spectrum based error corrector for 454 sequencing data
AU - Wirawan, Adrianto
AU - Harris, Robert S.
AU - Liu, Yongchao
AU - Schmidt, Bertil
AU - Schröder, Jan
N1 - Funding Information: The authors thank the editor and the anonymous reviewers for their helpful and constructive comments which helped to improve the manuscript. JS received salary support from National Health and Medical Research Council (NHMRC) Program Grant (1054618). The research benefitted by the support from the Victorian State Government Operational Infrastructure Support and Australian Government NHMRC IRIISS.
N2 - 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.
AB - 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.
U2 - 10.1186/1471-2105-15-131
DO - 10.1186/1471-2105-15-131
JO - BMC Bioinformatics
JF - BMC Bioinformatics
Wirawan A, Harris RS, Liu Y, Schmidt B, Schröder J. HECTOR: A parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. BMC bioinformatics. 2014 May 6;15(1):131. doi: 10.1186/1471-2105-15-131