BS-virus-finder: virus integration calling using bisulfite sequencing data

Gigascience. 2018 Jan 1;7(1):1-7. doi: 10.1093/gigascience/gix123.


Background: DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation. Until now, only a few software tools have focused on virus integration using bisulfite sequencing data.

Findings: We have developed a new and easy-to-use software tool, named BS-virus-finder (BSVF, RRID:SCR_015727), to detect viral integration breakpoints in whole human genomes. The tool is hosted at

Conclusions: BS-virus-finder demonstrates high sensitivity and specificity. It is useful in epigenetic studies and to reveal the relationship between viral integration and DNA methylation. BS-virus-finder is the first software tool to detect virus integration loci by using bisulfite sequencing data.

Keywords: bisulfite sequencing; carcinogenesis; virus integration.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • Base Sequence
  • Cell Line, Tumor
  • DNA Methylation
  • DNA, Viral / genetics*
  • Epigenesis, Genetic
  • Genome, Human*
  • Hepatitis B virus / genetics*
  • Hepatocytes / metabolism
  • Hepatocytes / pathology
  • Hepatocytes / virology*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Sensitivity and Specificity
  • Software*
  • Sulfites / chemistry
  • Virus Integration*
  • Whole Genome Sequencing


  • DNA, Viral
  • Sulfites
  • hydrogen sulfite