Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.
PLoS One. 2013 May 24;8(5):e64465. doi: 10.1371/journal.pone.0064465. Print 2013.
Next generation sequencing (NGS) technologies allow us to explore virus interactions with host genomes that lead to carcinogenesis or other diseases; however, this effort is largely hindered by the dearth of efficient computational tools. Here, we present a new tool, VirusFinder, for the identification of viruses and their integration sites in host genomes using NGS data, including whole transcriptome sequencing (RNA-Seq), whole genome sequencing (WGS), and targeted sequencing data. VirusFinder's unique features include the characterization of insertion loci of virus of arbitrary type in the host genome and high accuracy and computational efficiency as a result of its well-designed pipeline. The source code as well as additional data of VirusFinder is publicly available at http://bioinfo.mc.vanderbilt.edu/VirusFinder/.
下一代测序（NGS）技术使我们能够探索病毒与宿主基因组相互作用导致癌变或其他疾病的机制；然而，这项工作在很大程度上受到缺乏有效计算工具的阻碍。在这里，我们提出了一种新的工具 VirusFinder，用于使用 NGS 数据（包括全转录组测序（RNA-Seq）、全基因组测序（WGS）和靶向测序数据）识别病毒及其在宿主基因组中的整合位点。VirusFinder 的独特功能包括对宿主基因组中任意类型病毒插入位点的特征描述，以及由于其精心设计的管道而具有的高精度和计算效率。VirusFinder 的源代码以及其他数据可在 http://bioinfo.mc.vanderbilt.edu/VirusFinder/ 上公开获取。
