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

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...

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Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Technical Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5788064/
https://www.ncbi.nlm.nih.gov/pubmed/29267855
http://dx.doi.org/10.1093/gigascience/gix123
Descripción
Sumario: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.

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