John Sealy School of Medicine, The University of Texas Medical Branch, Galveston, TX 77550, USA.
Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550, USA.
Bioinformatics. 2022 Sep 15;38(18):4420-4422. doi: 10.1093/bioinformatics/btac522.
Recombination is an essential driver of virus evolution and adaption, giving rise to new chimeric viruses, structural variants, sub-genomic RNAs and defective RNAs. Next-generation sequencing (NGS) of virus samples, either from experimental or clinical settings, has revealed a complex distribution of recombination events that contributes to intrahost diversity. We and others have previously developed alignment tools to discover and map these diverse recombination events in NGS data. However, there is no standard for data visualization to contextualize events of interest, and downstream analysis often requires bespoke coding.
We present ViReMaShiny, a web-based application built using the R Shiny framework to allow interactive exploration and point-and-click visualization of viral recombination data provided in BED format generated by computational pipelines such as ViReMa (Viral-Recombination-Mapper).
The application is hosted at https://routhlab.shinyapps.io/ViReMaShiny/ with associated documentation at https://jayeung12.github.io/. Code is available at https://github.com/routhlab/ViReMaShiny.
Supplementary data are available at Bioinformatics online.
重组是病毒进化和适应的重要驱动因素，导致新的嵌合病毒、结构变体、亚基因组 RNA 和缺陷 RNA 的产生。对来自实验或临床环境的病毒样本进行下一代测序（NGS），揭示了复杂的重组事件分布，这有助于宿主内多样性。我们和其他人之前开发了对齐工具，以在 NGS 数据中发现和映射这些多样化的重组事件。然而，目前没有用于可视化数据的标准来上下文化有意义的事件，下游分析通常需要定制编码。
我们提出了 ViReMaShiny，这是一个使用 R Shiny 框架构建的基于网络的应用程序，允许以 BED 格式交互式探索和点击可视化由计算管道（如 ViReMa（病毒重组映射器））生成的病毒重组数据。
该应用程序托管在 https://routhlab.shinyapps.io/ViReMaShiny/ 上，并在 https://jayeung12.github.io/ 上提供相关文档。代码可在 https://github.com/routhlab/ViReMaShiny 上获得。
补充数据可在生物信息学在线获得。
