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- Publisher Website: 10.18632/oncotarget.4187
- Scopus: eid_2-s2.0-84940736866
- PMID: 26087185
- WOS: WOS:000360969200023
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Article: Virus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability
Title | Virus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability |
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Authors | |
Keywords | Viral integration Next-generation sequencing Viral integration site detection Breakpoint detection |
Issue Date | 2015 |
Publisher | Impact 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? |
Abstract | Viral 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 Identifier | http://hdl.handle.net/10722/212082 |
ISSN | 2016 Impact Factor: 5.168 2023 SCImago Journal Rankings: 0.789 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Ho, DWH | - |
dc.contributor.author | Sze, MF | - |
dc.contributor.author | Ng, IOL | - |
dc.date.accessioned | 2015-07-21T02:22:25Z | - |
dc.date.available | 2015-07-21T02:22:25Z | - |
dc.date.issued | 2015 | - |
dc.identifier.citation | Oncotarget, 2015, v. 6, n. 25, p. 20959-20963 | - |
dc.identifier.issn | 1949-2553 | - |
dc.identifier.uri | http://hdl.handle.net/10722/212082 | - |
dc.description.abstract | Viral 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.language | eng | - |
dc.publisher | Impact Journals LLC. The Journal's web site is located at http://www.impactjournals.com/oncotarget/index.html | - |
dc.relation.ispartof | Oncotarget | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | Viral integration | - |
dc.subject | Next-generation sequencing | - |
dc.subject | Viral integration site detection | - |
dc.subject | Breakpoint detection | - |
dc.title | Virus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability | - |
dc.type | Article | - |
dc.identifier.email | Ho, DWH: dwhho@hku.hk | - |
dc.identifier.email | Sze, MF: karensze@hkucc.hku.hk | - |
dc.identifier.email | Ng, IOL: iolng@hku.hk | - |
dc.identifier.authority | Ng, IOL=rp00335 | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.18632/oncotarget.4187 | - |
dc.identifier.pmid | 26087185 | - |
dc.identifier.scopus | eid_2-s2.0-84940736866 | - |
dc.identifier.hkuros | 244515 | - |
dc.identifier.volume | 6 | - |
dc.identifier.issue | 25 | - |
dc.identifier.spage | 20959 | - |
dc.identifier.epage | 20963 | - |
dc.identifier.isi | WOS:000360969200023 | - |
dc.publisher.place | United States | - |
dc.identifier.issnl | 1949-2553 | - |