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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​