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VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue
Open accessAbstract
Summary: We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on whole-transcriptome sequencing (RNA-Seq) data of 256 human cancer samples from The Cancer Genome Atlas. Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using whole-genome sequencing data of human tissue. Availability: VirusSeq has been implemented in PERL and is available at http://odin.mdacc.tmc.edu/∼xsu1/VirusSeq.html. Contact: xsu1@mdanderson.org Supplementary information: Supplementary data are available at Bioinformatics online.
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Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma
Feng, H., Shuda, M., Chang, Y., & Moore, P. S. (2008) · Science · doi:10.1126/science.1152586 · Cited by 3,208
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Metadata
- Authors
- Chen, Y., Yao, H., Thompson, E. J., Tannir, N. M., Weinstein, J. N., & Su, X.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-11-17
- Volume
- 29
- Issue
- 2
- Pages
- 266-267
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2158274053
- Cited by
- 158
- References
- 1
- FWCI
- 3.25
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Chen, Y., Yao, H., Thompson, E. J., Tannir, N. M., Weinstein, J. N., & Su, X. (2013). VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue. Bioinformatics. https://doi.org/10.1093/bioinformatics/bts665
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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