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

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  • Shengjie Gao, BGI-Shenzhen, Shenzhen 518083, China
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  • Xuesong Hu, BGI-Shenzhen, Shenzhen 518083, China
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  • Fengping Xu, China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.
  • ,
  • Changduo Gao, College of Computer Science & Technology, Qingdao University, Qingdao 266071, China.
  • ,
  • Kai Xiong, University of Copenhagen, Department of Veterinary Clinical and Animal Sciences, Frederiksberg C, Copenhagen, Denmark ; kkf@sund.ku.dk.
  • ,
  • Xiao Zhao, BGI Education Center, University of Chinese Academy of Sciences.
  • ,
  • Haixiao Chen, China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.
  • ,
  • Shancen Zhao, James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.
  • ,
  • Mengyao Wang, BGI-Shenzhen, Shenzhen 518083, China
  • ,
  • Dongke Fu, Forensics Genomics International (FGI), BGI-Shenzhen, Shenzhen 518083, China.
  • ,
  • Xiaohui Zhao, College of Mathematics & Statistics, Changsha University of Science & Technology, Changsha 410114, China.
  • ,
  • Jie Bai, BGI-Shenzhen, Shenzhen 518083, China
  • ,
  • Likai Mao, BGI-Shenzhen, Shenzhen 518083, China
  • ,
  • Bo Li, Forensics Genomics International (FGI), BGI-Shenzhen, Shenzhen 518083, China., BGI-Shenzhen, Shenzhen 518083, China
  • ,
  • Song Wu, The Affiliated Luohu Hospital of Shenzhen University, Shenzhen University, Shenzhen 518000, China.
  • ,
  • Jian Wang, BGI-Shenzhen, Shenzhen 518083, China
  • ,
  • Shengbin Li, College of Medicine and Forensics, XJTU. Xian China.
  • ,
  • Huangming Yang, BGI Education Center, University of Chinese Academy of Sciences.
  • ,
  • Lars Bolund
  • Christian N S Pedersen

Background: DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling SNP, DMR, and ASM. Until now, only a few software tools focus 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 https://github.com/BGI-SZ/BSVF.

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.

Original languageEnglish
JournalGigaScience
ISSN2047-217X
DOIs
Publication statusPublished - 2018

    Research areas

  • Journal Article

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