JBrowse 2

JBrowse 2 is a pluggable, open-source genome browser. It runs as a web app, a desktop app (Mac, Windows, Linux), and as embeddable React components. It offers linear, circular, dotplot, synteny, and spreadsheet views, with track types for alignments (BAM/CRAM), variants and structural variants, quantitative/coverage, and more, plus a grammar of graphics that plots any file's fields from config.

The web app is "static-site compatible": it is pure client-side JS, CSS, and HTML, so it can be hosted anywhere with no server. The stack is React, TypeScript, and @jbrowse/mobx-state-tree.

Installing and running

• Desktop app: downloads
• Web app: web quickstart
• Embedded React components: embed a Linear Genome View

Documentation

• Documentation home has the user guide, config guide, developer guide, and CLI reference
• Tutorials are step-by-step guides grouped by topic (synteny, SVs, methylation, RNA-seq, and more)
• FAQ

Examples

• Feature list

Contact

• Homepage
• Contact and office hours

Publications

• JBrowse 2: a modular genome browser with views of synteny and structural variation (2023) https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02914-z
• Setting up the JBrowse 2 genome browser (2024) https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.1120
• Setting up JBrowse 2 for Visualizing Genome Synteny (2025) https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.70236
• Proteins in the Genome Browser: Integration of Phylogenies, Alignments, and Structures With Nucleotide-level Evidence in JBrowse 2 (2026) https://www.sciencedirect.com/science/article/abs/pii/S0022283626000185

Contributing

See CONTRIBUTING.md to get set up, and agent-docs/ARCHITECTURE.md for the rendering pipeline and core architecture.