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Updated: May 15, 2026

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
Published on: March 22, 2016
ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base
Jing-Woei Li1, Raymond Wan, Chi-Shing Yu
1School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.
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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