• 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

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 jbr

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 git

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

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) @c

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 m

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)#

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](https://github.co

• 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 s

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 t

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

Thanks to everying for reporting and helping fix these issues!

Downloads#

• v4.0.4

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](https://jbrowse.org/jb2/docs/quickstart_

There are a lot of improvements large and small

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

![Screenshot From 2025-12-02 09-20-40](https://github.com/user-attachments/assets/0bd4475e-0f7e-4e09-

JBrowse 2 genome hubs https://genomes.jbrowse.org#

We created a new website at https://genomes.jbrowse.org that features new JBrowse 2 instances for over 50,000 species. This massive effort is primarily driven by bulk loading data curated by the UCSC genome browser team, both their main browsers and GenArk hubs, which have data for thousands of NCBI RefSeq (curated) and GenBank genomes

All of these JBrowse 2 instances are available on both the web and on the desktop app

Users can even browse "synteny views" betwe

Downloads#

• v3.6.5

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.

3.6.5 (2025-09-11)#

:rocket: Enhancement#

• #5142 Load jbrowse config passed as CLI arg to jbrowse desktop, and

Please see the release notes below

Downloads#

• v3.6.4

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.

3.6.4 (2025-07-21)#

:rocket: Enhancement#

• core, web-core
  • #5101 Add concept of loading a JBrowse 2 config.json

Downloads#

• v3.6.3

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.

This release includes a relatively large refactoring of the CLI to use built-in node.js arg parsing, but other than that, these are just small bugfixes and usability improvements. Please see release notes for more info

Downloads#

• v3.6.2

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.

3.6.2 (2025-07-10)#

:rocket:#

Better dropdown menus#

In previous releases, the dropdown submenus would close the instant your mouse left their boundaries, but now, they stay open until you select a menu item or click away. This can be very useful when accessing nested submenus

Ability to customize root configuration#

We added the ability for plugins to add new entries to the root configuration. This now makes it possible to add easy-to-access configuration for your plugin. Example:

export default class MsaViewPlugi

The synteny view can display long alignments, including insertions and deletions. However, particularly in chain files, the specific "insertion/deletion" markers are less meaningful as a large insertion+deletion pair is often used to connect more high-scoring alignments across large distances

Screenshot before/after toggling the setting to show only matches

Re#

Improved gene name searching#

We added a fuzzy finder library (uFuzzy) that helps prioritize the results returned by our text search (e.g. trix), so gene name searching should provide much more relevant results

Updated documentation with new screenshots#

We updated gallery (https://jbrowse.org/jb2/gallery/) with new screenshots and live links, and are rolling out updated screenshots throughout the docs pages to be more up to date and high quality

Misc#

We also fixed a bug in methylation/modifications rendering that c