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

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

Shengjie Gao  1   2   3   4   5   6 , Xuesong Hu  2   3 , Fengping Xu  3   7   8 , Changduo Gao  9 , Kai Xiong  10 , Xiao Zhao  2   11 , Haixiao Chen  3   8 , Shancen Zhao  3   4 , Mengyao Wang  3 , Dongke Fu  2 , Xiaohui Zhao  12 , Jie Bai  3 , Likai Mao  3 , Bo Li  2   3 , Song Wu  5 , Jian Wang  3 , Shengbin Li  2   13   14 , Huangming Yang  3   4   11 , Lars Bolund  6 , Christian N S Pedersen  1
Affiliations

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

Shengjie Gao et al. Gigascience. .

Abstract

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 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.

Keywords: bisulfite sequencing; carcinogenesis; virus integration.

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Figures

Figure 1:
Figure 1:
The illustration of bisulfite-altered sequence to the original.
Figure 2:
Figure 2:
Principal types of mapping reads around the viral integration site.
Figure 3:
Figure 3:
A demo plot of 1 viral integration cluster in its pre-insertion form.
See this image and copyright information in PMC

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