Wan Yinan, Renner Daniel W, Albert Istvan, Szpara Moriah L
The Huck Institutes of the Life Sciences, University Park, PA 16802 USA.
Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802 USA.
Gigascience. 2015 Apr 28;4:19. doi: 10.1186/s13742-015-0060-y. eCollection 2015.
Advances in next generation sequencing make it possible to obtain high-coverage sequence data for large numbers of viral strains in a short time. However, since most bioinformatics tools are developed for command line use, the selection and accessibility of computational tools for genome assembly and variation analysis limits the ability of individual labs to perform further bioinformatics analysis.
We have developed a multi-step viral genome assembly pipeline named VirAmp, which combines existing tools and techniques and presents them to end users via a web-enabled Galaxy interface. Our pipeline allows users to assemble, analyze, and interpret high coverage viral sequencing data with an ease and efficiency that was not possible previously. Our software makes a large number of genome assembly and related tools available to life scientists and automates the currently recommended best practices into a single, easy to use interface. We tested our pipeline with three different datasets from human herpes simplex virus (HSV).
VirAmp provides a user-friendly interface and a complete pipeline for viral genome analysis. We make our software available via an Amazon Elastic Cloud disk image that can be easily launched by anyone with an Amazon web service account. A fully functional demonstration instance of our system can be found at http://viramp.com/. We also maintain detailed documentation on each tool and methodology at http://docs.viramp.com.
新一代测序技术的进步使得在短时间内获取大量病毒株的高覆盖度序列数据成为可能。然而，由于大多数生物信息学工具是为命令行使用而开发的，用于基因组组装和变异分析的计算工具的选择和可及性限制了各个实验室进行进一步生物信息学分析的能力。
我们开发了一个名为VirAmp的多步骤病毒基因组组装流程，它结合了现有工具和技术，并通过基于网络的Galaxy界面将它们呈现给终端用户。我们的流程允许用户轻松、高效地组装、分析和解读高覆盖度病毒测序数据，这在以前是不可能的。我们的软件为生命科学家提供了大量基因组组装及相关工具，并将当前推荐的最佳实践自动化整合到一个易于使用的单一界面中。我们用来自人类单纯疱疹病毒（HSV）的三个不同数据集测试了我们的流程。
VirAmp为病毒基因组分析提供了一个用户友好的界面和完整的流程。我们通过亚马逊弹性云磁盘镜像提供我们的软件，任何拥有亚马逊网络服务账户的人都可以轻松启动它。我们系统的一个功能齐全的演示实例可在http://viramp.com/找到。我们还在http://docs.viramp.com上维护了关于每个工具和方法的详细文档。
