Summary: 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.
Availability: VFS is distributed under GPL version 3 at http://hkbic.cuhk.edu.hk/software/viralfusionseq
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582262 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btt011 | DOI Listing |
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