Skip to main content

v3.1.0 Release

· 3 min read

This release adds several interesting features including

Sticky view headers and pinned tracks​

We created a new UI where the "view header" stays visible even when scrolling the page.

We also added the ability to "pin" tracks in the linear genome view, which also stay visible when scrolling the page.

Cluster multi-quantitative tracks​

Motivated by the clustering workflow in the Multi-variant viewer, a similar feature was added to the multi-quantitative track

To do this, we sample the data according to the current zoom level (otherwise, it would create very large matrices at per-base resolution) and then provide an R script the user can run to cluster the data

Before clustering image

After clustering Screenshot From 2025-03-11 00-25-06

Simplify some adapter configuration​

The configuration system has a lot of complex substructure, but in this release we created the ability to supply a simplified config, and the results will be auto-determined

For example

{
  "type": "AlignmentsTrack",
  "trackId": "volvox_alignments",
  "name": "volvox-sorted.bam",
  "assemblyNames": ["volvox"],
  "adapter": {
    "type": "BedGraphTabixAdapter",
    "bedGraphGzLocation": {
      "uri": "file.bed.gz"
    },
    "index": {
      "location": {
        "uri": "file.bed.gz.tbi"
      }
    }
  }
}

after

{
  "type": "AlignmentsTrack",
  "trackId": "volvox_alignments",
  "name": "volvox-sorted.bam",
  "assemblyNames": ["volvox"],
  "adapter": {
    "type": "BedGraphTabixAdapter",
    "uri": "file.bed.gz"
  }
}

The CLI tools and other systems will continue to output the verbose version for the time being, but this simplified system will be handy to anyone who does hand-coding of the configuration

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 3.1.0

3.1.0 (2025-03-14)​

🚀 Enhancement​

  • Other
    • #4876 Allow inferring default values of adapter urls to simplify config.json (@cmdcolin)
    • #4875 Add sample data from HGSVCv3 to 1000 genomes demo and config_demo (@cmdcolin)
    • #4880 Allow selecting track error messages with click and drag (@cmdcolin)
    • #4882 Allow clustering multi-wiggle tracks on the fly (@cmdcolin)
    • #4874 Use a '012' matrix to improve clustering of genotypes (@cmdcolin)
  • core
    • #4871 Add deletion, insertion, skip, softclip, hardclip to theme (@cmdcolin)
  • app-core, core, product-core

🐛 Bug Fix​

Committers: 2​