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 https://github.com/GMOD/jbrowse-components/pull/5468 for an overview/comment thread

Downloads#

• v4.3.0

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

Changes since v4.2.1 (2026-04-27)#

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

Hi all,

This release fixes the ability to search by gene name using the &loc= URL param since v4, fixes some MM tag parsing errors in BAM/CRAM files, and a couple other misc changes

Important extra note: We are rapidly iterating on a WebGPU/WebGL based accelerated rendering system for JBrowse 2, and are aporoaching 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 https://github.com/GMOD/jbrowse-components/pull/5468 for an overview/comment thread

Downloads#

• v4.2.1

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

Changes since v4.2.0 (2026-04-16)#

bug#

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

Re-release as trusted publishing

Downloads#

• v4.2.0

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

Changes since v4.1.15 (2026-04-02)#

bug#

• Fix inconsistent sanitization causing broken trix index file paths on desktop (#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

Hi all, This is a basic bug fix release

Fixes some small potential bugs

It also tests out using github actions CI to publish the release artifacts

Downloads#

• v4.1.16

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

Changes since v4.1.15 (2026-04-02)#

bug#

• Fix inconsistent sanitization causing broken trix index file paths on desktop (#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

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

Downloads#

• v4.1.15

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

Changes since v4.1.14 (2026-03-08)#

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

This release fixes a bug with parsing BAM files with large headers on the v4 branch

Downloads#

• v4.1.14

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

Changes since v4.1.13 (2026-02-20)#

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

Updates app name on mac again and tries to improve the auto-update workflow

Downloads#

• v4.1.13

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

Changes since v4.1.12 (2026-02-19)#

Bugfixes

Downloads#

• v4.1.4

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

Changes since v4.1.3 (2026-01-27)#

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#

• Remove node-fetch library (#5486) @cmdcolin
• Typescriptify webpack configs and build scripts (#5485) @cmdcolin
• Export fetchResults from linear-genome-view (#5482) @hextraza
• 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
• Remove electron-builder (#5457) @cmdcolin
• Make the loading bars occupy full track height (#5451) @cmdcolin

internal#

• Update jsdom and @mui/x-data-grid (#5484) @cmdcolin
• Bump dependencies (#5469) @cmdcolin
• Add more backward compatibility exports (#5467) @garrettjstevens

This release includes several important bugfixes including fixes for:

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

Downloads#

• v4.1.3

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

Changes since v4.1.1 (2026-01-22)#

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

enhancement#

• Cache configurations by snapshot identity (#5450) @cmdcolin

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

Downloads#

• v4.1.1

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

Changes since v4.0.4 (2026-01-17)#

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