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v2.3.1 Release

· 4 min read

Hello all! This release adds some great new features!

  • New "arc" and "read cloud" alignments track modes which render long range connections between read pairs/split reads. These views have a big impact on being able to visualize structural variants.

  • We now automatically optimize the "prefix size" for our trix indexes created by jbrowse text-index which should help solve issues with slow text searching.

  • We now refer to many pluggable elements by a "display name" instead of the coded class name so we have instead of "LinearGCContentDisplay" -> "GC content display".

New alignments track displays​

We created a new display mode that changes the "pileup" of reads into "arcs" which connects both paired-end reads and split-long read alignments.

New track menu showing the ability to replace the "lower panel" with arc display or read cloud display

The arc view and read cloud view rendering across discontinuous displayedRegions

A zoomed in view of long-reads (top) and paired-end reads (bottom) at the breakpoint of a large deletion

Easily toggleable "compact" view of alignments​

We now have an easily toggleable compact setting on alignments tracks (previously had to manually change feature height)

Optimized prefix size for text search indexing​

Previously, if indexing long gene IDs with jbrowse text-index it would often be slow because the "trix" format is generally optimized for short gene symbols. We added the --prefixSize parameter in previous jbrowse versions to allow optimizing for specific gene ID lengths, but this was sort of a magic number. Now, jbrowse text-index will automatically calculate the --prefixSize if none is provided, which tries to get an even ~64kb bin size. Let us know how it goes for your data!

Re-install the CLI tools with e.g. npm install -g @jbrowse/cli to get the latest version with this feature.

Moved "Track Hub Registry" plugin to plugin store​

We removed the "Track Hub Registry" plugin, which was previously a "core plugin", to the plugin store. This will allow us to update the plugin over time and respond better to issues when they change their remote API.

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.

🚀 Enhancement​

  • Other
    • #3403 Reduce overplotting on dotplot grid lines and other misc improvements (@cmdcolin)
    • #3381 Add method for cache busting requests to the config file in jbrowse-web (@cmdcolin)
    • #3384 Add method to more easily create compact view of alignments (@cmdcolin)
  • core
    • #3391 Allow arc display to connect to "unpaired" positions using RNEXT/PNEXT or SA tag (@cmdcolin)
    • #3387 Small UI tweaks for add track workflow (@cmdcolin)
    • #3358 Create new "arc" display type to show long range connections between paired-end and split-reads (@cmdcolin)
  • text-indexing
    • #3385 Optimize prefix size for text indexing automatically (@cmdcolin)

🐛 Bug Fix​

  • Other
    • #3407 Remove trackhub registry plugin from core plugins, moved to plugin store (@cmdcolin)
    • #3406 Fix loading connection tracks from connections that don't specify assemblyNames in config (@cmdcolin)
    • #3390 Fix positioning within large alignments for query->target LGV synteny navigation (@cmdcolin)
    • #3388 Fix search result that matches synonyms that matches multiple locations (@cmdcolin)
  • core
    • #3404 Fix double-render of some synteny features (@cmdcolin)
    • #3401 Remove y-scalebar rendering placeholder values in blank and loading states (@cmdcolin)
    • #3389 Fix issue where snackbar would not show up when same error message is triggered multiple times (@cmdcolin)

📝 Documentation​

  • core
  • Other
    • #3383 Add note to user guide about variant callers that can be used for SV inspector (@cmdcolin)

🏠 Internal​

  • __mocks__, core, text-indexing
    • #3400 Reduce peerDependency warnings from installing dev environment (@cmdcolin)
  • core

Committers: 1​