Release v4.3.0

This release adds a variety of small bugfixes

• Loads bedMethyl as multiquantitativetrack automatically
• Improved/unified behavior of the &highlight= matching the bookmark highlight behavior
• Fixed specification of multi-level synteny views from URL query params (now takes a two dimensional array of string[][], where each pairwise comparison level takes a list of syntenytrack trackIds)
• Add featureHeight param for alignmentstracks in jb2image CLI tool
• Website overhaul! Uses astro instead of docusaurus now
• Standardized discordant pair coloring with IGV based coloring (navy,green,teal) Let us know if you have any feedback

Additionally, the new GPU refactor is ongoing and we are interested in hearing from users that would like to test. Please contact jbrowse2@berkeley.edu for more info or visit #5468 for an overview/comment thread

bug

• Fix highlight chip not being clickable (#5554) @cmdcolin

documentation

• Change website from docusaurus to astro (#5550) @cmdcolin
• More doc improvements from claude code audit of docs (#5549) @cmdcolin
• Add documentation to help with visualizing and interpreting SVs in jbrowse (#5547) @cmdcolin

Release v4.2.1

Hi all,

This release fixes the ability to search by gene name using the &loc= URL param which was broken after the release v4, and also fixes some MM tag parsing errors in BAM/CRAM files, and some issues with weird labels when zoomed in on variants.

Important extra note: We are rapidly iterating on a WebGPU/WebGL based accelerated rendering system for JBrowse 2, and are approaching a final product.

We are interested to hear from users and model organism database admins interested in beta testing and trying it out. The entire result is a relatively large code change, but we are aiming for minimal breaking changes for end users of the app.

Please contact jbrowse2@berkeley.edu for more info or visit #5468 for an overview/comment thread

bug

• Fix nav to search string via &loc= (#5544) @cmdcolin

Release v4.2.0

Hello all,
This release fixes a small number of bugs.

It is just a fun tech note but our releases now use 'trusted publishing' https://docs.npmjs.com/trusted-publishers

Thanks and happy browsing

bug

• Fix inconsistent filename sanitization causing broken trix file paths on desktop when track contains slash (#5540) @cmdcolin

enhancement

• Create github actions based publishing workflow using NPM trusted publishing (#5530) @cmdcolin
• Create supertrack/folder concept, browse categories/folders with faceted selector, and plugin hooks for custom track selection UI (#5515) @cmdcolin
  Done in 0.30s.

Release v4.1.15

This release fixes some issues where the alignments track was not scrollable, and some other misc issues

bug

• Fix MM tag ambiguity codes not being recognized (#5529) @cmdcolin
• Fix when using refname aliases for chromosome names in displayedRegions list (#5522) @cmdcolin
• Fix arc tracks with custom jexl crashing (#5513) @cmdcolin
• Fix alignments tracks not being able to vertically scroll since v4.1.4 (#5512) @cmdcolin
• Fix HTTP 416 errors by replacing http-range-fetcher with simpler fetcher (#5505) @cmdcolin

enhancement

• Update dependencies (#5527) @cmdcolin
• Add debounce to hierarchical search text field (#5517) @cmdcolin
• Use Element setHTML if available (#5507) @cmdcolin

Release v4.1.14

This release fixes a bug with parsing BAM files with large headers on the v4 branch and a couple other small things

bug

• Bump @gmod/jexl for multi-expression fix (#5494) @cmdcolin
• Fix custom multi-sample variant label coloring loss after clustering (#5493) @cmdcolin
• Fix displaying 'sanitized html' in faceted data grid (#5492) @cmdcolin

enhancement

• Optionally disable gene heuristic manually via config for BED/BigBed type files (#5495) @cmdcolin

Release v4.1.11

Hello all, this is a minor bugfix and feature release

Please note that we are in the process of migrating to WebGL/WebGPU, which includes smooth zooming and improved performance. Please feel free to contact us or visit #5468
for more information and early preview

bug

• Fix trackname not showing up in search results dialog (#5480) @cmdcolin
• Use summaryScoreMode for stats range calculation (#5475) @cmdcolin
• Fix "Add track" showing track in mismatched assembly view (#5474) @cmdcolin
• Fix floating labels in svg exports (#5465) @cmdcolin
• Fix show all regions with many small elided regions (#5454) @cmdcolin

enhancement

• Allow searching metadata in faceted track selector (#5477) @cmdcolin
• Search result extension point (#5476) @cmdcolin
• Add PNG export option to the 'Export SVG' dialog (#5463) @cmdcolin
• Add hierarchical tree sidebar to multiwiggle clusterings (#5459) @cmdcolin
• Make the loading bars occupy full track height (#5451) @cmdcolin

internal

• Remove electron-builder (#5457) @cmdcolin
• Update jsdom and @mui/x-data-grid (#5484) @cmdcolin
• Bump dependencies (#5469) @cmdcolin
• Add more backward compatibility exports (#5467) @garrettjstevens
• Remove node-fetch library (#5486) @cmdcolin
• Typescriptify webpack configs and build scripts (#5485) @cmdcolin
• Export fetchResults from linear-genome-view (#5482) @hextraza

Release v4.1.3

This release includes several important bugfixes including fixes for:

a) the scrolling being extremely choppy when zoomed in since v4.0.3
b) jbrowse text-index not indexing all tracks by default

Full changelog

bug

• Revert css based --var scrolling due to visual glitches at large bp offsets (#5449) @cmdcolin
• Fix jbrowse-cli text-index not working without --tracks parameter (#5446) @cmdcolin
• Add E2E test for jbrowse img (#5443) @cmdcolin
• Fix jbrowse-img for ESM css loader and setupEnv. (#5441) @Yihuki
• Stop token refactoring and gene glyph speed up when zoomed in (#5450) @cmdcolin

Release v4.1.1

Hello all,
This is a minor release but contains a couple great new features, and some important bugfixes. Please see the release notes below

Local files are preserved even after page refresh in jbrowse-web

When users of jbrowse-web open files from their local machine, it can continue to work after page refresh. This is currently a Chrome only feature facilitated by the FileSystemFileHandle API https://developer.mozilla.org/en-US/docs/Web/API/FileSystemFileHandle

Add advanced track configuration via the URL bar

Previously, users could launch tracks by supplying a list of trackIds in the URL e.g. &tracks=track1,track2. Now, users can supply an array of JSON params https://jbrowse.org/jb2/docs/urlparams/#advanced-track-configuration

Add linkage disequilibrium viewer

In an effort to expand the utility of our variant visualization capabilities, we integrated a built-in linkage disequilibrium viewer for multi-sample variant tracks. This can load data from multi-sample variant files or PLINK output files. This can plot r^2 and D' with a variety of visual customization options

See the full changelog below for more info

bug

• Minor fixes for genbank and gff3 file export (#5435) @cmdcolin
• Fix issues with large VCF files not displaying in v4.0.4 (#5432) @cmdcolin
• Add testing for remote file fetching in text-index (#5429) @cmdcolin
• Fix text-index from remote gz file. (#5427) @Yihuki

enhancement

• Add stack trace to jbrowse desktop text indexing failures (#5436) @cmdcolin
• Add config.json slots for multi-sample variant displays (#5434) @cmdcolin
• Add examples of using the Core-preProcessConfig extension point (#5433) @cmdcolin
• Bump to @gmod/cram v8 for qual speed and memory optimization (#5430) @cmdcolin
• Allow supplying initial display parameters when using URL query param API (#5426) @cmdcolin
• Allow custom jexl functions to be used in filters (#5425) @cmdcolin
• Add type:"module" to package.json's to complete ESM conversion (#5422) @cmdcolin
• Add testing for electron app using windows github action runner and fix text indexing on windows (#5421) @cmdcolin
• Create system for visualizing linkage disequilibrium from VCF and PLINK output files (#5420) @cmdcolin
• Add ability to reload local files across page using FileSystemFileHandle API (#5419) @cmdcolin
• Add re-exports to enable embedded apps to use webworkers after v4 (#5418) @cmdcolin

Release v4.0.4

Hello all,

this release fixes some bugs reported by users in v4.0.3 including those related to

• using workspaces in jbrowse desktop
• searching and text indexing gff3 on desktop
• using mouseover tooltips on the new canvas features

Thanks to everyone for reporting and helping fix these issues!

bug

• Fix desktop text indexing workflow and search for GFF3 files, and add testing (#5411) @cmdcolin
• Fix errors using 'duplicate session' and viewing recent sessions (#5408) @cmdcolin
• Fix tiled window manager/workspaces not working on desktop (#5406) @cmdcolin

enhancement

• Misc refactors and improvements (#5415) @cmdcolin
• Allow specifying tiled window layout via the URL (#5409) @cmdcolin
• Cluster haplotypes in multi-sample variant viewer (#5403) @cmdcolin
• Add selenium tests for jbrowse desktop (#5110) @cmdcolin

Release v4.0.3

Hello all! We are happy to announce this new major version update to JBrowse 2

There are a lot of improvements large and small!

PS we created a new survey to gather responses about people's experiences, please feel free to fill it out and/or share with others! https://forms.gle/okejv948EZU87E4M7 (anonymous responses are ok!)

Without further ado, here are some highlights in this new version

New "Collapsed introns" view

Users can right-click a gene and launch a 'Collapsed introns' view that focuses on just the exonic regions. The RNA-seq alignments work with this view also, with sashimi arcs connecting across the different regions

New "Canvas features" track type

We have replaced the SVG feature renderer with a new HTML5 canvas feature renderer. This has improved user experience and also comes with new functionality including:

• Per-transcript mouseover and feature clicks
• Ability to show only the "Longest transcript" for gene glyphs with many sub-transcripts
• Improved performance
• Directional chevrons

Screenshot showing the "Longest transcript" option

Alignments track performance improvements

Our BAM and CRAM parsers were updated with a variety of performance optimizations. We analyzed the entire stack and added

• low level binary for parsing CIGAR strings
• using WASM for parsing
• using mosdepth style coverage calculations
• improved speed for deep RNA-seq data

And much more

Alignments track mouseovers and new features

We also added many usability improvements to the alignments tracks like adding the ability to mouseover and click individual insertions, mismatches, deletions, etc.

Users can also optionally turn off drawing mismatches entirely...sometimes it's not what you care to see!

"Linked read display" improvements

In v3.7.0 we announced the "Linked read display" mode (https://jbrowse.org/jb2/blog/2025/11/07/v3.7.0-release/#create-linked-read-display-for-alignments-tracks) which connects paired end or split long reads. This new release allows drawing mismatches on the reads, and generally behaves a lot like the normal alignments track!

Screenshot showing an inversion with split long reads (the red->blue->red chain indicates a single split long read flipping orientation in the middle) and paired-end short reads (blue and green reads indicate aberrant pairing)

Display color legends on screen

We added the ability to show legends on a variety of display types, which will help users understand the meaning of colors on the screen!

"Save track data"

Users can now export data in the visible region in a variety of formats, tailored to the track type and file type of interest. This was a commonly requested feature, so we are excited to finally solve it

Simplified configuration

Users no longer have to explicitly supply 'sequenceAdapter' to BAM and CRAM files. It will infer the sequence adapter from the assembly. Anyone who directly works with JBrowse configuration files will benefit from this simplification!

Screenshot showing a simplified config for a CRAM track

Much faster load time for large tracklists

Previously, when a JBrowse instance had more than a couple thousand tracks, the startup time would slow down dramatically. We made internal changes to our track loading that now makes these load times virtually instant now! This was enabled by making track configuration models instantiated only when the track is opened, which plugin authors should be aware of

Graph showing the load time of different tracklist sizes in v3.7.0 and v4.0.0, showing runaway showness with v3.7.0 after just a couple thousand tracks that is now under control in v4.0.0

Easily filter variant samples by genotype

This allows users to easily filter the variants in the feature detail widget by genotype. It can also be toggled to filter by 'dosage' which is helpful for polyploid organisms

New "Workspaces" feature for tiled window management!

We added the Dockview (https://dockview.dev) window manager to the app interface, so you can now create left-right splits, top-bottom splits, new tabs, and more in jbrowse web and desktop. This enables a large variety of extra layouts compared with the previous vertical-stack-only limitation of previous JBrowse 2 versions!

Screenshot showing left-right split

Improved user-experience when side-scrolling

Wiggle and Hi-C tracks will now stay on the screen while new renderings (e.g. change to y-axis scale) are re-computing. It is a subtle change that we hope improves user-experience!

Breaking changes

There are a large number of internal changes, and it would be hard to fully enumerate all the changes, but some of the changes include

• Splitting renderProps (for webworker renderer) and renderingProps (main thread)
• Changing mobx-state-tree to @jbrowse/mobx-state-tree https://github.com/GMOD/mobx-state-tree
• Changing jexl to @jbrowse/jexl https://github.com/GMOD/jexl
• Removal of @jbrowse/plugin-svg, automatically remapping to CanvasFeatureRenderer
• Make all packages "pure-ESM", may affect node.js usage

A variety of other internal changes took place. If you see any problems after migration, please let us know and we will be happy to work with you to help

User survey

We have started a new survey here https://forms.gle/dy41TWmKe8KPRews7 to help gather user experiences with JBrowse. We know that it is not always easy to get the courage to create github issues but any feedback large or small is welcome!

bug

• Fix smaller genomic region being shown when using &tracklist=true URL params (#5388) @cmdcolin
• Fix color by CDS / calculation of phase on BED12/bigbed files (#5384) @cmdcolin
• Fix hot module reload losing app state (#5374) @cmdcolin
• Fix issue where multiple sub-menus could open up at once (#5308) @cmdcolin
• Avoid changing displayed regions set when using "Center at feature" in synteny view (#5281) @cmdcolin
• Avoid 'polynomial regex' in assembly name parsing (#5258) @cmdcolin
• Fix export of SVG hanging if track had error (#5234) @cmdcolin
• Reduce coarseStripHTML regex complexity to address codeql warning (#5233) @cmdcolin
• Fix click-and-drag starting from a inter-region padding block (#5226) @cmdcolin
• Add cancellation stop tokens for linear read arc/cloud displays (#5221) @cmdcolin

dependencies

• Update to jest 30 (#5223) @cmdcolin

documentation

• Add PAG 2026 user tutorial (#5340) @garrettjstevens

enhancement

• Show full dotplot when zoomed all the way out (#5387) @cmdcolin
• Switch to pnpm as package manager and add ESM "exports" to packages (#5382) @cmdcolin
• Re-organize 'track action' menu items into a submenu (#5378) @cmdcolin
• Remove BroadcastChannel from SessionLoader (#5375) @cmdcolin
• Allow plugins to make custom radio items for synteny import forms (#5373) @cmdcolin
• Allow easily filtering samples in the variant feature details by genotype/dosage (#5366) @cmdcolin
• Allow clicking transcript subfeatures of a gene glyph (#5363) @cmdcolin
• Add --excludeTracks to jbrowse text-index (#5354) @cmdcolin
• Use custom 'jexl' fork with multi-statement evaluation and template strings (#5353) @cmdcolin
• Search indexedDB for old sessions when using a local- type URL (#5346) @cmdcolin
• Filter out defaults from session snapshots (#5339) @cmdcolin
• Add general concept for showing legends on tracks (#5337) @cmdcolin
• Improve mouseover and clicking on mismatches/modifications on SNPCoverage (#5336) @cmdcolin
• Create layout optimizations for deep RNA-seq data (#5330) @cmdcolin
• Filter sashimi arcs by score (#5329) @cmdcolin
• Multiple optimizations for alignments tracks (#5326) @cmdcolin
• Add WASM code for unzipping in CRAM, BAM, BigWig, Tabix, etc. (#5320) @cmdcolin
• Optimizations for multi-wiggle tracks (#5318) @cmdcolin
• Add optional directional 'chevrons' to the gene glyphs (#5317) @cmdcolin
• Collapse introns transcript selector (#5316) @cmdcolin
• Avoid "import form flash" during loading (#5314) @cmdcolin
• Avoid drawing tick labels that overlap block boundaries (#5312) @cmdcolin
• Create pluggable glyph system for canvas feature renderer (#5311) @cmdcolin
• Create optimizations for alignments track (#5310) @cmdcolin
• Improve bigwig Y-scalebar label legibility (#5307) @cmdcolin
• Make BAM and CRAM adapters use assembly sequence adapter (#5305) @cmdcolin
• Add gridlines option for SVG export (#5303) @cmdcolin
• Aggregate insertion stats in on SNP coverage track (#5301) @cmdcolin
• Add "tiled window manager" ...