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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 tutorials, or hosted genomes at Genome Hubs.

Run JBrowse

Use JBrowse

Configure and host

Embed and script

Extend JBrowse

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, samplot: 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: for proving GPU powered and grammar of graphics techniques
  • Every other genome visualization developer
  • UCSC genome browser - For their genome browser and open data sharing, enabling genomes.jbrowse.org

Contact

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

Enjoy!