ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution.

Insertional mutagenesis from virus infection is an important pathogenic risk for the development of cancer. Despite the advent of high-throughput sequencing, discovery of viral integration sites and expressed viral fusion events are still limited. Here, we present ViralFusionSeq (VFS), which combines soft-clipping information, read-pair analysis and targeted de novo assembly to discover and annotate viral-human fusions. VFS was used in an RNA-Seq experiment, simulated DNA-Seq experiment and re-analysis of published DNA-Seq datasets. Our experiments demonstrated that VFS is both sensitive and highly accurate. VFS is distributed under GPL version 3 at http://hkbic.cuhk.edu.hk/software/viralfusionseq

Citation

Jing-Woei Li, Raymond Wan, Chi-Shing Yu, Ngai Na Co, Nathalie Wong, Ting-Fung Chan. ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution. Bioinformatics (Oxford, England). 2013 Mar 01;29(5):649-51

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PMID: 23314323

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