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v4.1.1 Release

· 3 min read

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