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Article: rMFilter: acceleration of long read-based structure variation calling by chimeric read filtering

TitlerMFilter: acceleration of long read-based structure variation calling by chimeric read filtering
Authors
Issue Date2017
PublisherOxford University Press (OUP): Policy B - Oxford Open Option B. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
Citation
Bioinformatics, 2017, v. 33 n. 17, p. 2750-2752 How to Cite?
AbstractMotivation: Long read sequencing technologies provide new opportunities to investigate genome structural variations (SVs) more accurately. However, the state-of-the-art SV calling pipelines are computational intensive and the applications of long reads are restricted. Results: We propose a local region match-based filter (rMFilter) to efficiently nail down chimeric noisy long reads based on short token matches within local genomic regions. rMFilter is able to substantially accelerate long read-based SV calling pipelines without loss of effectiveness. It can be easily integrated into current long read-based pipelines to facilitate SV studies. Availability and implementation: The C ++ source code of rMFilter is available at https://github.com/hitbc/rMFilter . Contact: ydwang@hit.edu.cn.
Persistent Identifierhttp://hdl.handle.net/10722/264708
ISSN
2017 Impact Factor: 5.481
2015 SCImago Journal Rankings: 4.643
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorLiu, B-
dc.contributor.authorJiang, T-
dc.contributor.authorYiu, SM-
dc.contributor.authorLi, JY-
dc.contributor.authorWang, Y-
dc.date.accessioned2018-10-24T01:49:47Z-
dc.date.available2018-10-24T01:49:47Z-
dc.date.issued2017-
dc.identifier.citationBioinformatics, 2017, v. 33 n. 17, p. 2750-2752-
dc.identifier.issn1367-4803-
dc.identifier.urihttp://hdl.handle.net/10722/264708-
dc.description.abstractMotivation: Long read sequencing technologies provide new opportunities to investigate genome structural variations (SVs) more accurately. However, the state-of-the-art SV calling pipelines are computational intensive and the applications of long reads are restricted. Results: We propose a local region match-based filter (rMFilter) to efficiently nail down chimeric noisy long reads based on short token matches within local genomic regions. rMFilter is able to substantially accelerate long read-based SV calling pipelines without loss of effectiveness. It can be easily integrated into current long read-based pipelines to facilitate SV studies. Availability and implementation: The C ++ source code of rMFilter is available at https://github.com/hitbc/rMFilter . Contact: ydwang@hit.edu.cn.-
dc.languageeng-
dc.publisherOxford University Press (OUP): Policy B - Oxford Open Option B. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/-
dc.relation.ispartofBioinformatics-
dc.subject.meshGenome, Human-
dc.subject.meshGenomic Structural Variation-
dc.subject.meshGenomics-
dc.subject.meshHumans-
dc.subject.meshSequence Analysis, DNA-
dc.titlerMFilter: acceleration of long read-based structure variation calling by chimeric read filtering-
dc.typeArticle-
dc.identifier.emailYiu, SM: smyiu@cs.hku.hk-
dc.identifier.authorityYiu, SM=rp00207-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1093/bioinformatics/btx279-
dc.identifier.pmid28482046-
dc.identifier.scopuseid_2-s2.0-85044525788-
dc.identifier.hkuros292128-
dc.identifier.volume33-
dc.identifier.issue17-
dc.identifier.spage2750-
dc.identifier.epage2752-
dc.identifier.isiWOS:000408772700021-
dc.publisher.placeUnited Kingdom-

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