Cantor Michael, Nordberg Henrik, Smirnova Tatyana, Hess Matthias, Tringe Susannah, Dubchak Inna
Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
University of California at Davis, One Shields Avenue, Davis, CA, 95616-8521, USA.
BMC Bioinformatics. 2015 Apr 28;16(1):130. doi: 10.1186/s12859-015-0566-4.
Metagenomics, the sequencing of DNA collected from an entire microbial community, enables the study of natural microbial consortia in their native habitats. Metagenomics studies produce huge volumes of data, including both the sequences themselves and metadata describing their abundance, assembly, predicted functional characteristics and environmental parameters. The ability to explore these data visually is critically important to meaningful biological interpretation. Current genomics applications cannot effectively integrate sequence data, assembly metadata, and annotation to support both genome and community-level inquiry.
Elviz (Environmental Laboratory Visualization) is an interactive web-based tool for the visual exploration of assembled metagenomes and their complex metadata. Elviz allows scientists to navigate metagenome assemblies across multiple dimensions and scales, plotting parameters such as GC content, relative abundance, phylogenetic affiliation and assembled contig length. Furthermore Elviz enables interactive exploration using real-time plot navigation, search, filters, axis selection, and the ability to drill from a whole-community profile down to individual gene annotations. Thus scientists engage in a rapid feedback loop of visual pattern identification, hypothesis generation, and hypothesis testing.
Compared to the current alternative of generating a succession of static figures, Elviz can greatly accelerate the speed of metagenome analysis. Elviz can be used to explore both user-submitted datasets and numerous metagenome studies publicly available at the Joint Genome Institute (JGI). Elviz is freely available at http://genome.jgi.doe.gov/viz and runs on most current web-browsers.
宏基因组学，即对从整个微生物群落收集的DNA进行测序，能够研究自然微生物群落的原生栖息地。宏基因组学研究产生大量数据，包括序列本身以及描述其丰度、组装、预测功能特征和环境参数的元数据。以可视化方式探索这些数据的能力对于有意义的生物学解释至关重要。当前的基因组学应用无法有效地整合序列数据、组装元数据和注释，以支持基因组和群落水平的探究。
Elviz（环境实验室可视化工具）是一个基于网络的交互式工具，用于对组装好的宏基因组及其复杂的元数据进行可视化探索。Elviz允许科学家在多个维度和尺度上浏览宏基因组组装，绘制诸如GC含量、相对丰度、系统发育归属和组装重叠群长度等参数。此外，Elviz还支持使用实时绘图导航、搜索、过滤器、轴选择以及从整个群落概况深入到单个基因注释的功能进行交互式探索。因此，科学家能够参与到一个视觉模式识别、假设生成和假设检验的快速反馈循环中。
与当前生成一系列静态图表的替代方法相比，Elviz可以大大加快宏基因组分析的速度。Elviz可用于探索用户提交的数据集以及联合基因组研究所（JGI）公开提供的众多宏基因组研究。Elviz可在http://genome.jgi.doe.gov/viz免费获取，并在大多数当前的网络浏览器上运行。
