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
Figure showing improved speed on short read alignments of the refactor (this
release) vs main (which was v2.1.7)