Re-release as trusted publishing
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.
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
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 fixes some issues where the alignments track was not scrollable and other misc issues
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 fixes a bug with parsing BAM files with large headers on the v4 branch
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.
Updates app name on mac again and tries to improve the auto-update workflow
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.
Bugfixes
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.
electron-builder
(#5457) @cmdcolinThis release includes several important bugfixes including fixes for:
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.
Hello all, This is a minor release but contains a couple great new features, and some important bugfixes. Please see the release notes below
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
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
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
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.
Hello all, this fixes some minor bugs reported in the v4.0.3 including those related to
Thanks to everying for reporting and helping fix these issues!
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.
Hello all! We are happy to announce this new major version update to JBrowse 2
There are a lot of improvements large and small
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
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:
Screenshot showing the "Longest transcript" option
Our BAM and CRAM parsers were updated with a variety of performance optimizations. We analyzed the entire stack and added
And much more
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!
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)
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!
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
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
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 slowness with v3.7.0 after just a couple thousand tracks that is now under control in v4.0.0
Users can now easily filter the samples in the variants feature detail widget by genotype. The filter can match exact genotype or 'dosage' which is helpful for polyploid organisms
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
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!
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
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
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!
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.
depcheck warnings
(#5257) @cmdcolin