Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, United States.
Bioinformatics. 2024 Jun 3;40(6). doi: 10.1093/bioinformatics/btae369.
Ribosome profiling is a widely-used technique for measuring ribosome occupancy at nucleotide resolution. However, the need to analyze this data at nucleotide resolution introduces unique challenges in data visualization and analyses.
In this study, we introduce RiboGraph, a dedicated visualization tool designed to work with .ribo files, a specialized and efficient format for ribosome occupancy data. Unlike existing solutions that rely on large alignment files and time-consuming preprocessing steps, RiboGraph operates on a purpose designed compact file type. This efficiency allows for interactive, real-time visualization at ribosome-protected fragment length resolution. By providing an integrated toolset, RiboGraph empowers researchers to conduct comprehensive visual analysis of ribosome occupancy data.
Source code, step-by-step installation instructions and links to documentation are available on GitHub: https://github.com/ribosomeprofiling/ribograph. On the same page, we provide test files and a step-by-step tutorial highlighting the key features of RiboGraph.
核糖体谱是一种广泛使用的技术，用于以核苷酸分辨率测量核糖体占有率。然而，需要以核苷酸分辨率分析此数据会在数据可视化和分析方面带来独特的挑战。
在这项研究中，我们引入了 RiboGraph，这是一种专门设计的可视化工具，可与.ribo 文件配合使用，.ribo 文件是一种用于核糖体占有率数据的专用且高效的格式。与依赖于大型对齐文件和耗时预处理步骤的现有解决方案不同，RiboGraph 基于专门设计的紧凑文件类型运行。这种效率允许以核糖体保护片段长度分辨率进行交互式、实时可视化。通过提供集成的工具集，RiboGraph 使研究人员能够对核糖体占有率数据进行全面的可视化分析。
源代码、逐步安装说明和文档链接可在 GitHub 上获得：https://github.com/ribosomeprofiling/ribograph。在同一页面上，我们提供测试文件和逐步教程，突出显示了 RiboGraph 的关键功能。
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