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Bioinformatics. 2013 Mar 1;29(5):649-51. doi: 10.1093/bioinformatics/btt011. Epub 2013 Jan 12.

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

Author information

1
School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.

Abstract

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

PMID:
23314323
PMCID:
PMC3582262
DOI:
10.1093/bioinformatics/btt011
[Indexed for MEDLINE]
Free PMC Article

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