Bolduc Benjamin, Youens-Clark Ken, Roux Simon, Hurwitz Bonnie L, Sullivan Matthew B
Department of Microbiology, The Ohio State University, Columbus, OH, USA.
Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ, USA.
ISME J. 2017 Jan;11(1):7-14. doi: 10.1038/ismej.2016.89. Epub 2016 Jul 15.
Microbes affect nutrient and energy transformations throughout the world's ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as 'Apps') for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature.
微生物影响着全球生态系统中的养分和能量转化，然而它们是在病毒的限制下进行这些活动的。在复杂的群落中，病毒宏基因组（病毒组）测序正在改变我们量化病毒多样性及其影响的能力。尽管一些瓶颈，例如参考基因组较少和病毒组学非定量等问题已经得到克服，但目前缺乏集中的数据集和专门的工具阻碍了病毒组学被广泛应用于回答基本的生态学问题。在此，我们介绍iVirus，这是一个利用CyVerse网络基础设施提供对病毒组学工具和数据集访问的社区资源。iVirus数据共享库包含来自1866个样本和73个项目的原始数据和处理后的数据，这些样本和项目源自全球海洋考察，以及现有的和旧有的公共储存库。通过CyVerse发现环境，用户可以使用现有的分析工具（称为“应用程序”的软件应用）对这些数据集进行查询，以进行组装、开放阅读框预测和注释，以及使用几个专门为分析病毒组而开发的新应用程序。由于应用程序基于网络并由CyVerse超级计算资源提供支持，它们能够为广大用户群体进行可扩展的分析。最后，一个用例场景记录了如何将这些进展应用于新数据。这个不断发展的iVirus资源应该有助于研究人员将病毒组学作为另一种工具来阐明病毒在自然界中的作用。
