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v3.7.0 Release

· 7 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

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

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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)

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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
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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 From 2025-10-25 12-11-35

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/)

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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​