School of Life Sciences, Tsinghua University, Beijing, China.
BMC Bioinformatics. 2023 Aug 9;24(1):309. doi: 10.1186/s12859-023-05438-2.
Visualizing genome coverage is of vital importance to inspect and interpret various next-generation sequencing (NGS) data. Besides genome coverage, genome annotations are also crucial in the visualization. While different NGS data require different annotations, how to visualize genome coverage and add the annotations appropriately and conveniently is challenging. Many tools have been developed to address this issue. However, existing tools are often inflexible, complicated, lack necessary preprocessing steps and annotations, and the figures generated support limited customization.
Here, we introduce ggcoverage, an R package to visualize and annotate genome coverage of multi-groups and multi-omics. The input files for ggcoverage can be in BAM, BigWig, BedGraph and TSV formats. For better usability, ggcoverage provides reliable and efficient ways to perform read normalization, consensus peaks generation and track data loading with state-of-the-art tools. ggcoverage provides various available annotations to adapt to different NGS data (e.g. WGS/WES, RNA-seq, ChIP-seq) and all the available annotations can be easily superimposed with ' + '. ggcoverage can generate publication-quality plots and users can customize the plots with ggplot2. In addition, ggcoverage supports the visualization and annotation of protein coverage.
ggcoverage provides a flexible, programmable, efficient and user-friendly way to visualize and annotate genome coverage of multi-groups and multi-omics. The ggcoverage package is available at https://github.com/showteeth/ggcoverage under the MIT license, and the vignettes are available at https://showteeth.github.io/ggcoverage/ .
可视化基因组覆盖度对于检查和解释各种下一代测序（NGS）数据至关重要。除了基因组覆盖度之外，基因组注释在可视化中也很关键。虽然不同的 NGS 数据需要不同的注释，但如何适当地、方便地可视化基因组覆盖度并添加注释是具有挑战性的。已经开发了许多工具来解决这个问题。然而，现有的工具往往不够灵活、复杂，缺乏必要的预处理步骤和注释，并且生成的图形支持的自定义程度有限。
在这里，我们介绍了 ggcoverage，这是一个用于可视化和注释多组和多组学基因组覆盖度的 R 包。ggcoverage 的输入文件可以是 BAM、BigWig、BedGraph 和 TSV 格式。为了更好的可用性，ggcoverage 提供了可靠且高效的方法来使用最先进的工具进行读归一化、共识峰生成和轨道数据加载。ggcoverage 提供了各种可用的注释，以适应不同的 NGS 数据（例如 WGS/WES、RNA-seq、ChIP-seq），并且所有可用的注释都可以通过“ + ”轻松叠加。ggcoverage 可以生成出版质量的图形，用户可以使用 ggplot2 对图形进行自定义。此外，ggcoverage 支持蛋白质覆盖度的可视化和注释。
ggcoverage 提供了一种灵活、可编程、高效和用户友好的方法来可视化和注释多组和多组学的基因组覆盖度。ggcoverage 包可在 MIT 许可证下在 https://github.com/showteeth/ggcoverage 获得，演示文稿可在 https://showteeth.github.io/ggcoverage/ 获得。
