Introduction

JBrowse 2 is a pluggable, open-source genome browser that runs on the web, on the desktop, and embedded in your own app. Data is organized into assemblies (reference genomes) and tracks layered on top of them.

See the visualization gallery, or hosted genomes at Genome Hubs.

Run JBrowse#

• JBrowse web
• JBrowse desktop
• Embedded components

Use JBrowse#

• User guide
• Tutorials
• Feature overview
• FAQ

Configure and host#

• Config and session JSON
• Config guide
• Cookbook
• Supported file types
• Config reference
• @jbrowse/cli

Embed and script#

• Automating JBrowse
• URL query parameter API
• JBrowseR
• jbrowse-anywidget
• @jbrowse/img

Extend JBrowse#

• Developer guide
• Writing a plugin
• State model reference
• Exported functions

Prior art and credit#

JBrowse 2 stands on the shoulders of many great scientists that came before us. Points of reference:

• Savant genome browser: genome arcs
• Gap5 genome browser: the read cloud, a cousin of genome arcs
• Mummerplots: auto-diagonalization routines for better synteny figures
• minimap2 and the PAF format: the basis our synteny visualizations are built on
• samtools and the hts-specs community: a continued substrate for complex bioinformatics formats like BAM, CRAM and VCF
• pggb, cactus and the other pangenome tool developers: for proving pangenomics works
• chain2paf, paftools.js and the rest of the ecosystem that grew around PAF
• jcvi/MCScan: the easy protein-alignment synteny workflow we standardized around, whose .anchors and .blocks formats other programs (the OrthoFinder workflow among them) use to this day
• ReactJS, TypeScript, mobx-state-tree and the JavaScript community: building a bioinformatics ecosystem on the web is hard when most of the field works in other languages
• IGV and igv.js: much of the alignments track, particularly read pairing and modBAM color schemes, view as pairs, and link supplementary alignments
• D-GENIES: for establishing a very high quality, easy to use dotplot viewer
• GenomeSpy and HiGlass/Gosling: for proving WebGL powered browsers
• Every other genome visualization developer

Contact#

Ask questions on the GitHub discussions board, report a bug on GitHub issues, or contact us directly with suggestions and feedback.

Enjoy!