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v3.7.0 Release

· 6 min read

Hi everyone, This is a big release on many fronts! Here are some highlights

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" between the different hubs by opening a liftOver track, see https://genomes.jbrowse.org/demos/ for example

Screenshot of hg38 vs hs1, as seen in the demos page

Synteny and dotplot viewer improvements​

We added some new features to the dotplot and synteny view, including:

  • Opacity/transparency slider
  • Min length slider
  • Easy picker for new color schemes
  • Auto-diagonalization to reorder chromosomes
  • "Location markers" for helping see where you are in large alignments

A screenshot of the grape vs peach with "Color by Query" enabled in the dotplot and synteny view

Screenshot of the location markers, which help orient where you are in large alignments

Draw amino acids on Gene glyphs​

The setting "Color by CDS" added the ability to draw amino acid letters (and was thus renamed "Color by CDS and draw amino acids").

This can help with detailed investigations of protein structures, which is an area we are actively developing (see https://github.com/GMOD/proteinbrowser for more information)

Create 'Linked read display' for Alignments tracks​

Users can now see paired-end reads and supplementary alignments as linked entities using the "Linked reads display". This can be particularly useful for structural variant inspection.

We included a variety of specialized options to help users dig into their data, including:

  • Show/hide proper pairs
  • Show/hide 'singletons' (reads without pairs or supplementary alignments)
  • Coloring schemes that highlight misoriented pairs and abnormally large insert sizes
  • And more

Screenshot showing the "Linked reads display" with PacBio, Nanopore, and Illumina paired-end reads. The long reads with split alignments are colored salmon and light blue so that you can see the flip in orientation from positive to negative, and back to positive again. The short paired-end reads are colored navy and green to show the misoriented pairs

Screenshot showing a variety of SV types with our mock test data

Improved modified reads plotting​

Some of the code for handling modifications was given a fresh refactor, which fixed bugs with 'duplex' data where modifications are stored on both a positive and negative pass on the same read

Here is an example of a screenshot showing chromatin accessibility via introduced 6mA methylation from a Nanopore dataset (source: https://epi2me.nanoporetech.com/chromatin-acc-hg002/)

Conclusion​

Let us know if you have any feedback on these new features! Enjoy

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.

3.7.0 (2025-11-07)​

🚀 Enhancement​

  • core
    • #5201 Add 'bulk operations' to the multi-wiggle color editor (@cmdcolin)
    • #5197 Ability to make help text on menu items (@cmdcolin)
    • #5183 Add ability to link supplementary alignments and pairs (@cmdcolin)
    • #5136 Add ability to mouseover alignments tracks (@cmdcolin)
    • #4967 Add ability to connect to genark and UCSC browsers to jbrowse desktop (@cmdcolin)
  • Other
    • #5195 Add ability to adjust alpha, min alignment length, color scheme and option to diagonalize synteny plots (@cmdcolin)
    • #5196 Optimize gridlines component (@cmdcolin)
    • #5188 Add searchable header bar to breakpoint split view (@cmdcolin)
    • #5186 Fix the display of 'duplex' sequence modifications on BAM files and default to only showing mods >=10% (@cmdcolin)
    • #5182 Add deletions and mismatches to the pileup mouseover (@cmdcolin)
    • #5178 Add CDS protein numbering to glyphs (@cmdcolin)
    • #5169 Use more accurate alpha blending for synteny view (@cmdcolin)
    • #5162 Add some support for SVLEN to infer the END of a variant from VCF 4.5 (@cmdcolin)
    • #5122 Link to "Genomes" in jbrowse website header bar (@cmdcolin)

🐛 Bug Fix​

  • core
  • Other
    • #5175 Fix for tracks from wrong assembly showing up in track list when using connections (@cmdcolin)
    • #5170 Update gff-nostream dependency to fix features not found errors (@cmdcolin)
    • #5169 Use more accurate alpha blending for synteny view (@cmdcolin)
    • #5164 Fix SV inspector data grid filtering synchronization with circular view (@cmdcolin)
    • #5161 Add missing "tmp" dependency to @jbrowse/cli package.json (@garrettjstevens)

🏠 Internal​

Committers: 2​

v3.6.5 Release

· 2 min read

This release contains a couple small bugfixes related to refresh-less installing plugins

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.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.6.5

3.6.5 (2025-09-11)​

🚀 Enhancement​

  • #5142 Load jbrowse config passed as CLI arg to jbrowse desktop, and support .jbrowse file extension (@amorison)
  • #5144 Convert GC content calculation to rolling average for speed improvement (@cmdcolin)

🐛 Bug Fix​

🏠 Internal​

Committers: 3​

v3.6.4 Release

· 2 min read

Hi all, This release adds a couple bugfixes

Please see the release notes below

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.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.6.4

3.6.4 (2025-07-21)​

🚀 Enhancement​

  • core, web-core
    • #5101 Add concept of loading a JBrowse 2 config.json as a connection, and add extension point to allow plugins to lazy load configs (@cmdcolin)
  • Other
  • product-core

🐛 Bug Fix​

  • core
    • #5120 Generalize parse line by line function to fix bed, gff3, and other types of files with no trailing newline (@cmdcolin)
    • #5111 Fix issue where multiple cascading submenus could be opened at once (@cmdcolin)
  • Other
    • #5118 Avoid clearing click-and-drag rubberband boundaries onMouseOut to fix "Zoom to region", bookmark region, etc. (@cmdcolin)
    • #5115 Fix 'Add track widget' bug when changing input filename (@cmdcolin)

Committers: 2​

v3.6.3 Release

· One min read

Hi all, This quick release fixes issues with opening local files on JBrowse Desktop

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.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.6.3

Done in 0.81s.

v3.6.2 Release

· 3 min read

Hello all,

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​

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.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.6.2

3.6.2 (2025-07-10)​

🚀 Enhancement​

  • Other
  • core
    • #5095 Fix alpha rendering of SVG renderer box stroke/fill (@cmdcolin)
    • #5086 Add status message reporting for synteny view loading (@cmdcolin)

🐛 Bug Fix​

  • Other
    • #5100 Fix adding .pif file from dotplot and linear synteny import form (@cmdcolin)
    • #5098 Also migrate the linear-comparative-view rubberband tooltip to default MUI tooltip to avoid potential UI hangs (@cmdcolin)
    • #5097 Fix make pif on large files throwing ENOBUFS error in certain cases (@cmdcolin)
    • #5089 Additional type check to catch non-string MM tags from older Cell Ranger version BAM files (@haessar)
    • #5085 Fix rubberband getting stuck under certain conditions (@cmdcolin)
    • #5080 Fix crash on multi-wiggle importer on jbrowse-web (@cmdcolin)
  • core
    • #5095 Fix alpha rendering of SVG renderer box stroke/fill (@cmdcolin)

📝 Documentation​

  • #5099 Update readme with short description of what JBrowse 2 is, new links, and publications (@cmdcolin)

🏠 Internal​

  • __mocks__, app-core, core
    • #5077 Bump generic-filehandle with mock for test environment (@cmdcolin)

Committers: 2​

v3.5.1 Release

· 4 min read

Hi all, This has a number of small bugfixes and features. Here are a couple highlights

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 MsaViewPlugin extends Plugin {
  name = 'MyPlugin'

  install(pluginManager: PluginManager) {}

  configure(pluginManager: PluginManager) {}

  rootConfigurationSchema(pluginManager: PluginManager) {
    return {
      mything: ConfigurationSchema('MyConfig', {
        greetings: {
          type: 'string',
          defaultValue: 'hello world',
        },
      }),
    }
  }
}

A user could then customize their greeting in a new way like

{
  "assemblies": [...],
  "tracks": [...],
  "plugins": [...],
  "mything": {
    "greetings": "hello jbrowsers"
  }
}

This can then be used in your code by readConfObject(session.jbrowse, ['mything','greetings'])

Here is an example used by the MSA view plugin https://github.com/GMOD/jbrowse-plugin-msaview/blob/7027f01abe2b4253fd2a250021d2b13a1b4f2fce/src/index.ts#L37-L59

We anticipate that this will enable new and easier plugin customizations

More small updates​

See the release notes below for more info

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.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.5.1

3.5.1 (2025-06-05)​

🚀 Enhancement​

  • Other
    • #5064 Optimize fetching many small sequences from IndexedFasta (e.g. MSA datasets) (@cmdcolin)
    • #5059 Canonicalize refNames in search results (@cmdcolin)
    • #5056 Use assembly displayName on synteny header and ruler (@garrettjstevens)
    • #5050 Use standard sessionId for linear synteny view to reduce data re-fetching (@cmdcolin)
  • app-core, core, embedded-core
    • #5063 Improve usability of dropdown menus by making submenus not disappear immediately onMouseLeave (@cmdcolin)
  • core
  • app-core, core
    • #5044 Allow plugins to register entries onto the root configuration (@cmdcolin)

🐛 Bug Fix​

📝 Documentation​

🏠 Internal​

  • Other
  • core
    • #5061 Modularize some integration tests for launching views (@cmdcolin)

Committers: 2​

v3.5.0 Release

· 3 min read

Allow user to draw only matches in synteny view​

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

image image

Screenshot before/after toggling the setting to show only matches

Removal of the "Start screen" from jbrowse-web​

This release removes the "start screen" from jbrowse-web. Instead of showing the start screen, users are just dropped straight into the main jbrowse 2 interface. This will hopefully "drop users into the action" faster.

Bug fixes​

Some notable bug fixes include

  • Fix for loading bigwig files created by bigtools (a newer Rust-based bigwig toolkit)
  • Fix for certain breakpoint split view workflows fetching too much data and freezing

Feel free to let us know if you have any feedback

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.

yarn run v1.22.18 $ lerna-changelog --silent --silent --next-version 3.5.0

3.5.0 (2025-05-27)​

🚀 Enhancement​

  • #5042 Avoid inferring CDS subfeatures from non-coding gene pred features (@cmdcolin)
  • #5035 Use trash icon for uninstall in plugin store, and add version number string (@cmdcolin)
  • #4735 Remove jbrowse-web start screen (@cmdcolin)
  • #5025 Allow hiding insertion and deletion in synteny view to help chain file visualization (@cmdcolin)

🐛 Bug Fix​

  • Other
    • #5037 Check that breakpoint split view is ready before fetching to avoid crash/large data fetching (@cmdcolin)
    • #5033 Bump @gmod/bbi to fix loading bigwig files from bigtools (@cmdcolin)
    • #5024 Fix lines crossing over view headers in breakpoint split view by only setting sticky view headers on top-level views (@cmdcolin)
  • core

🏠 Internal​

  • core
  • Other
    • #5036 Remove the async keyword from BaseLinearDisplayModel (@cmdcolin)

Committers: 2​

v3.4.0 Release

· 4 min read

Hello all, this release adds a small set of features and bugfixes

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 caused crashes in v3.2.0-v3.3.0 and updated Electron to v36 (which now uses GTK4 on linux)

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.

yarn run v1.22.18 $ lerna-changelog --silent --silent --next-version 3.4.0

3.4.0 (2025-05-13)​

🚀 Enhancement​

  • core
    • #5018 Avoid serializing large features to sessions to fix quota exceeded errors in localstorage (@cmdcolin)
    • #5010 Add mouseover metadata for fields in the base feature widget (@cmdcolin)
    • #4998 Add padding to the genomic window of search result hits (@cmdcolin)
    • #4995 Add uFuzzy to improve gene name search (@cmdcolin)
    • #4983 Update some data parser packages for ESM compat (@cmdcolin)
    • #4980 Synthesize displayId if none provided in display config (@cmdcolin)
    • #4972 Support cytoband bed files starting with "#" (@cmdcolin)
  • Other
    • #5008 Allow parsing non-indexed BED files larger than 512MB (@cmdcolin)
    • #4997 Better message for "quota exceeded" message from localstorage (@cmdcolin)
    • #4974 Minor optimizations in multi-sample variant rendering (@cmdcolin)
    • #4973 Add basic cytoband for Drosophila (@cmdcolin)
    • #4970 Dynamically toggle wheel-scroll normalization to improve touchpad pinch-to-zoom usage (@cmdcolin)

🐛 Bug Fix​

  • core
    • #5013 Fix UCSC chain parsing which have header lines (@cmdcolin)
    • #4993 Fix re-export of @mui/material/styles, and re-export theme (@cmdcolin)
    • #4968 Fix theme augmentation for primary/secondary colors in v3.3.0 (@cmdcolin)
  • Other
    • #5004 Fix modifications rendering broken in v3.2.0 (@cmdcolin)
    • #4992 Fix mouseover for some variable width bigwig features (@cmdcolin)
    • #4984 Avoid rendering 'yellow' for low scores in wiggle density renderings with 'log-scale' enabled (@cmdcolin)
    • #4969 Avoid aggregating bigbed features with geneName === 'none' (@cmdcolin)

📝 Documentation​

🏠 Internal​

Committers: 2​

v3.3.0 Release

· 4 min read

Hello all,

This release adds a significant update to the multi-variant renderer that allows it to be used for visualizing structural variants Previously, all variants >10bp were filtered out, with the idea that overlapping variants are too difficult to interpret

This PR now allows drawing large structural variants in the multi-sample variant display type. It will actually draw long, even overlapping, structural variants!

image

Figure: Screenshot showing many SV calls over a 5Mbp+ region from the 3,202 human samples from the 1000 genomes project, with a large "inversion" variant showing the shaded triangles. The right side panel shows the feature details for this inversion variant showing the new genotype frequency panel, indicating about 47% of samples have a 'heterozygous' inversion call here

image

Loading a random track, and turning on the arc display, there are indications of a large variant for a random sample here (green and navy arcs indicate discordant read pairing associated with inversion)

We hope that you enjoy these new features! The visualizations may be visually complex but we hope it can be a magnifying glass to reveal important patterns of your datasets! Feel free to let us know if you have any feedback

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.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.3.0

3.3.0 (2025-04-18)​

🚀 Enhancement​

🐛 Bug Fix​

  • Other
    • #4929 Fix broken bigbed features when there is gene level aggregation (@cmdcolin)
  • core

📝 Documentation​

  • core
    • #4949 Controlling navigation of embedded component - storybook examples (@cmdcolin)
    • #4924 Add config docs for pre-processors with simplified config snapshots (@cmdcolin)
  • Other

🏠 Internal​

  • core

Committers: 1​

v3.2.0 Release

· 3 min read

Hello all,

This release includes a new ability to provide simplified snapshots to the linear genome view, a new built-in clustering method for genotypes, and more

In-app clustering​

In recent versions, we provided the ability to cluster genotype and multi-wiggle tracks, however we provided an R script for users to perform clustering externally and import the results

With this release, we have added a basic in-app clustering workflow, greatly improving the ease-of-use of this feature

image

Screenshot of the in-app clustering user interface

Renamed embedded packages and restored vanillajs builds​

We have renamed our embedded packages

  • Renamed @jbrowse/react-linear-genome-view -> @jbrowse/react-linear-genome-view2
  • Renamed @jbrowse/react-circular-genome-view -> @jbrowse/react-circular-genome-view2
  • Renamed @jbrowse/react-app -> @jbrowse/react-app2

Motivation: our vanillajs builds, which people often pointed to the "latest" release on from CDN networks, were no longer able to be updated in a backwards compatible way.

Therefore, we have renamed the packages, and updated tutorials.

This allows us to continue updating the package without any breakage for existing users. Please let us know if you run into any issues!

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.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.2.0

3.2.0 (2025-03-22)​

🚀 Enhancement​

  • core
    • #4919 Add in-app clustering method for multi-wiggle tracks (@cmdcolin)
    • #4909 Add ability to load refNameAliases from chromAliases.bb file (@cmdcolin)
    • #4906 Add in-app clustering method for genotype matrix (@cmdcolin)
  • Other
    • #4914 Allow looking up header column by name for RefNameAliases (@cmdcolin)
    • #4910 Allow refNameColumn in RefNameAliasAdapter to override the default displayed refnames (@cmdcolin)
    • #4907 Simplified snapshot API for initial navigation of LGV (@cmdcolin)
  • app-core, core, product-core, web-core
    • #4899 Add aborting to multi-variant rendering, multi-wiggle rendering (@cmdcolin)

🐛 Bug Fix​

  • #4920 Fix issue where multi-level linear synteny view would show a blank tracklist (@cmdcolin)
  • #4913 Fix parent aggregation in BigBed files using larger request window (@cmdcolin)
  • #4905 Fix bug where applying genotype clustering twice produces randomness (@cmdcolin)
  • #4897 Fix clustering for certain sets of bigwig files (@cmdcolin)

Committers: 1​