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

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...

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Bibliographic Details
Published in:Gigascience 2018-01, Vol.7 (1), p.1-7
Main Authors: Gao, Shengjie, Hu, Xuesong, Xu, Fengping, Gao, Changduo, Xiong, Kai, Zhao, Xiao, Chen, Haixiao, Zhao, Shancen, Wang, Mengyao, Fu, Dongke, Zhao, Xiaohui, Bai, Jie, Mao, Likai, Li, Bo, Wu, Song, Wang, Jian, Li, Shengbin, Yang, Huangming, Bolund, Lars, Pedersen, Christian N S
Format: Article
Language:English
Subjects:
Base Pairing
Base Sequence
Bisulfite
Breakpoints
Carcinogenesis
Carcinogens
Cell Line, Tumor
Deoxyribonucleic acid
DNA
DNA Methylation
DNA sequencing
DNA viruses
DNA, Viral - genetics
Epigenesis, Genetic
Epigenetics
Gene expression
Genome, Human
Genomes
Hepatitis B virus - genetics
Hepatocytes - metabolism
Hepatocytes - pathology
Hepatocytes - virology
High-Throughput Nucleotide Sequencing
Humans
Integration
Nucleotides
Polymorphism
Sensitivity and Specificity
Single-nucleotide polymorphism
Software
Sulfites - chemistry
Technical Note
Virus Integration
Viruses
Whole Genome Sequencing
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Summary: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. 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. 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.
ISSN:2047-217X
2047-217X
DOI:10.1093/gigascience/gix123