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
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