Zhao Guoyan, Wu Guang, Lim Efrem S, Droit Lindsay, Krishnamurthy Siddharth, Barouch Dan H, Virgin Herbert W, Wang David
Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.
Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
Virology. 2017 Mar;503:21-30. doi: 10.1016/j.virol.2017.01.005. Epub 2017 Jan 18.
The advent of Next Generation Sequencing (NGS) has vastly increased our ability to discover novel viruses and to systematically define the spectrum of viruses present in a given specimen. Such studies have led to the discovery of novel viral pathogens as well as broader associations of the virome with diverse diseases including inflammatory bowel disease, severe acute malnutrition and HIV/AIDS. Critical to the success of these efforts are robust bioinformatic pipelines for rapid classification of microbial sequences. Existing computational tools are typically focused on either eukaryotic virus discovery or virome composition analysis but not both. Here we present VirusSeeker, a BLAST-based NGS data analysis pipeline designed for both purposes. VirusSeeker has been successfully applied in several previously published virome studies. Here we demonstrate the functionality of VirusSeeker in both novel virus discovery and virome composition analysis.
新一代测序（NGS）技术的出现极大地提高了我们发现新型病毒以及系统定义给定样本中病毒谱的能力。此类研究已促成新型病毒病原体的发现，以及病毒组与多种疾病（包括炎症性肠病、严重急性营养不良和艾滋病毒/艾滋病）之间更广泛的关联。这些工作取得成功的关键在于拥有强大的生物信息学流程，以便对微生物序列进行快速分类。现有的计算工具通常要么专注于真核病毒发现，要么专注于病毒组组成分析，而不是两者兼顾。在此，我们介绍VirusSeeker，这是一种基于BLAST的NGS数据分析流程，专为这两个目的而设计。VirusSeeker已成功应用于此前发表的多项病毒组研究。在此，我们展示了VirusSeeker在新型病毒发现和病毒组组成分析方面的功能。
