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Article: Virus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability

TitleVirus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability
Authors
KeywordsViral integration
Next-generation sequencing
Viral integration site detection
Breakpoint detection
Issue Date2015
PublisherImpact Journals LLC. The Journal's web site is located at http://www.impactjournals.com/oncotarget/index.html
Citation
Oncotarget, 2015, v. 6, n. 25, p. 20959-20963 How to Cite?
AbstractViral integration into the human genome upon infection is an important risk factor for various human malignancies. We developed viral integration site detection tool called Virus-Clip, which makes use of information extracted from soft-clipped sequencing reads to identify exact positions of human and virus breakpoints of integration events. With initial read alignment to virus reference genome and streamlined procedures, Virus-Clip delivers a simple, fast and memory-efficient solution to viral integration site detection. Moreover, it can also automatically annotate the integration events with the corresponding affected human genes. Virus- Clip has been verified using whole-transcriptome sequencing data and its detection was validated to have satisfactory sensitivity and specificity. Marked advancement in performance was detected, compared to existing tools. It is applicable to versatile types of data including whole-genome sequencing, whole-transcriptome sequencing, and targeted sequencing. Virus-Clip is available at http://web.hku.hk/~dwhho/Virus-Clip.zip.
Persistent Identifierhttp://hdl.handle.net/10722/212082
ISSN
2015 Impact Factor: 5.008
2015 SCImago Journal Rankings: 2.294

 

DC FieldValueLanguage
dc.contributor.authorHo, DWH-
dc.contributor.authorSze, MF-
dc.contributor.authorNg, IOL-
dc.date.accessioned2015-07-21T02:22:25Z-
dc.date.available2015-07-21T02:22:25Z-
dc.date.issued2015-
dc.identifier.citationOncotarget, 2015, v. 6, n. 25, p. 20959-20963-
dc.identifier.issn1949-2553-
dc.identifier.urihttp://hdl.handle.net/10722/212082-
dc.description.abstractViral integration into the human genome upon infection is an important risk factor for various human malignancies. We developed viral integration site detection tool called Virus-Clip, which makes use of information extracted from soft-clipped sequencing reads to identify exact positions of human and virus breakpoints of integration events. With initial read alignment to virus reference genome and streamlined procedures, Virus-Clip delivers a simple, fast and memory-efficient solution to viral integration site detection. Moreover, it can also automatically annotate the integration events with the corresponding affected human genes. Virus- Clip has been verified using whole-transcriptome sequencing data and its detection was validated to have satisfactory sensitivity and specificity. Marked advancement in performance was detected, compared to existing tools. It is applicable to versatile types of data including whole-genome sequencing, whole-transcriptome sequencing, and targeted sequencing. Virus-Clip is available at http://web.hku.hk/~dwhho/Virus-Clip.zip.-
dc.languageeng-
dc.publisherImpact Journals LLC. The Journal's web site is located at http://www.impactjournals.com/oncotarget/index.html-
dc.relation.ispartofOncotarget-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectViral integration-
dc.subjectNext-generation sequencing-
dc.subjectViral integration site detection-
dc.subjectBreakpoint detection-
dc.titleVirus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability-
dc.typeArticle-
dc.identifier.emailHo, DWH: dwhho@hku.hk-
dc.identifier.emailSze, MF: karensze@hkucc.hku.hk-
dc.identifier.emailNg, IOL: iolng@hku.hk-
dc.identifier.authorityNg, IOL=rp00335-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.18632/oncotarget.4187-
dc.identifier.pmid26087185-
dc.identifier.scopuseid_2-s2.0-84940736866-
dc.identifier.hkuros244515-
dc.identifier.volume6-
dc.identifier.issue25-
dc.identifier.spage20959-
dc.identifier.epage20963-
dc.publisher.placeUnited States-

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