ViralFusionSeq

ViralFusionSeq is a software tool for discovering and annotating viral-human fusions from high-throughput sequencing data, which is important for identifying pathogenic risks for the development of cancer. The tool combines soft-clipping information, read-pair analysis, and targeted de novo assembly to achieve high accuracy and sensitivity. VFS has been tested on RNA-Seq and simulated DNA-Seq experiments and re-analysis of published DNA-Seq datasets.

Topic

Genomics;Gene structure;Mapping;Sequence assembly

Detail

  • Operation: Read pre-processing;Sequence alignment;Read mapping;Sequence assembly

  • Software interface: Command-line user interface

  • Language: Perl

  • License: -

  • Cost: Free

  • Version name: vfs-2016-08-17.r2

  • Credit: General Research Fund, a Theme-based Research Scheme from the Innovation and Technology Commission, Hong Kong Government, by Cluster Technology Ltd.

  • Input: -

  • Output: -

  • Contact: Ting-Fung Chan tf.chan@cuhk.edu.hk

  • Collection: -

  • Maturity: -

Publications

  • ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution.
  • Li JW, et al. ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution. ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution. 2013; 29:649-51. doi: 10.1093/bioinformatics/btt011
  • https://doi.org/10.1093/bioinformatics/btt011
  • PMID: 23314323
  • PMC: PMC3582262

Download and documentation

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