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

Please use this identifier to cite or link to this item: http://doi.org/10.25358/openscience-7352

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DC Field	Value	Language
dc.contributor.author	Wirawan, Adrianto	-
dc.contributor.author	Harris, Robert S.	-
dc.contributor.author	Liu, Yongchao	-
dc.contributor.author	Schmidt, Bertil	-
dc.contributor.author	Schröder, Jan	-
dc.date.accessioned	2022-07-11T10:28:05Z	-
dc.date.available	2022-07-11T10:28:05Z	-
dc.date.issued	2014	-
dc.identifier.uri	https://openscience.ub.uni-mainz.de/handle/20.500.12030/7366	-
dc.description.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 3.7x 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.	en_GB
dc.description.sponsorship	DFG, Open Access-Publizieren Universität Mainz / Universitätsmedizin	de
dc.language.iso	eng	de
dc.rights	CC BY	*
dc.rights.uri	https://creativecommons.org/licenses/by/2.0/	*
dc.subject.ddc	004 Informatik	de_DE
dc.subject.ddc	004 Data processing	en_GB
dc.title	HECTOR : a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data	en_GB
dc.type	Zeitschriftenaufsatz	de
dc.identifier.doi	http://doi.org/10.25358/openscience-7352	-
jgu.type.dinitype	article	en_GB
jgu.type.version	Published version	de
jgu.type.resource	Text	de
jgu.organisation.department	FB 08 Physik, Mathematik u. Informatik	de
jgu.organisation.number	7940	-
jgu.organisation.name	Johannes Gutenberg-Universität Mainz	-
jgu.rights.accessrights	openAccess	-
jgu.journal.title	BMC bioinformatics	de
jgu.journal.volume	15	de
jgu.pages.alternative	Art. 131	de
jgu.publisher.year	2014	-
jgu.publisher.name	BioMed central	de
jgu.publisher.place	London	de
jgu.publisher.uri	http://dx.doi.org/10.1186/1471-2105-15-131	de
jgu.publisher.issn	1471-2105	de
jgu.organisation.place	Mainz	-
jgu.identifier.pmid	24885381	-
jgu.subject.ddccode	004	de
opus.date.modified	2018-08-08T07:52:17Z	-
opus.subject.dfgcode	00-000	-
opus.organisation.string	FB 08: Physik, Mathematik und Informatik: Institut für Informatik	de_DE
opus.identifier.opusid	26769	-
opus.importsource	pubmed	-
opus.institute.number	0805	-
opus.metadataonly	false	-
opus.type.contenttype	Keine	de_DE
opus.type.contenttype	None	en_EN
opus.affiliated	Wirawan, Adrianto	-
opus.affiliated	Liu, Yongchao	-
opus.affiliated	Schmidt, Bertil	-
jgu.publisher.doi	10.1186/1471-2105-15-131	de
jgu.organisation.ror	https://ror.org/023b0x485
Appears in collections:	DFG-OA-Publizieren (2012 - 2017)

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