Visualizing Epigenomics in Jbrowse

Numerous genome browsers exist but very few offer customized support for epigenomics. I present a suite of plugins for epigenomics visualization in JBrowse, a fast and modern genome browser. Plugins have been created for DNA methylation, small RNA, and stranded coverage of chromatin immunoprecipitation sequencing (ChIP-seq). The plugin for DNA methylation supports multiple sequence contexts on a single track with each context in a different color. It also allows users to hide specific contexts for an individual track or all visible methylation tracks. Small RNA can be visualized the same as traditional mRNA-sequencing, but important information is lost. This plugin color codes reads based on length, displays reads on a positive and negative y-axis for strandedness, and includes multiple filtering options. Traditional ChIP-seq is displayed using coverage independent of strand. However, strandedness can be important for certain applications such as defining the location of transcription factor binding events. This plugin allows for stranded coverage in a single track. Finally, I have developed a plugin to help researchers document visualizations with high-quality screenshots. This offers significant benefits over current screenshot techniques, as it is entirely web-based and highly customizable for individual screenshots. These plugins are open-source and easily available, allowing for additional customizations based on user’s needs.