This is a release fixed some small issues with using typescript in the embedded components
See https://github.com/GMOD/jbrowse-components/releases/tag/v1.7.0 for the latest feature-set
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.
We are excited to announce the latest JBrowse release! This has many great features including
Floating feature labels, so if you are zoomed into the middle of a gene, the feature label hangs out alongside it on the left side of the screen! The results may not be pixel perfect in all cases (reverse complement labels can end up overlapping other features for example) but we hope this helps you see the labels for features that extend off the screen!
Figure showing the feature labels floating alongside gene even when you are zoomed into the feature
Upgraded build system for jbrowse-web and jbrowse-desktop to webpack 5, and added examples of using webpack 5 with embedded components. Webpack 5 results in smaller build sizes for jbrowse-web. For a typical session, amount of .js downloaded with gzip enabled in v1.6.9 is ~1.4MB, in v1.7.0 ~900kb (-500kb smaller). Without gzip enabled v1.6.9 4.8MB, v1.7.0 2.5MB (-2MB smaller). The result is largely due to better webworker bundling. See https://jbrowse.org/jb2/docs/embedded_components/ for webpack 5 examples in embedded components
Optimizations and improved visualization of paired-end reads in the breakpoint split view
Optimized linear synteny renderings with long CIGAR strings. These optimizations help viewing large alignments such as the CHM13-T2T-v2.0 assembly vs hg38 PAF file from https://github.com/marbl/CHM13#downloads (example here https://jbrowse.org/code/jb2/main/?config=test_data%2Fconfig_demo.json&session=share-0qD2-d_k4K&password=GF8Sk)
The "Assembly selector" dropdown box now remembers your last selection, so you can more easily return to your genome of interest
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.
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This is a re-release of 1.6.8 to fix the Mac build of JBrowse Desktop
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.
We are pleased to announce the v1.6.8 release!
This release includes a change to the default gene style to use boxes instead of "chevron" features, with a directional arrowhead
Before
After
Some additional highlights
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.
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This release fixes an issue with JBrowse Desktop on v1.6.6 where the first tracks to be opened would not load.
It also adds a speed optimization for BAM files (in some cases, 5x speed improvement seen in deep coverage files), and fixes a scroll issue on wiggle tracks!
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.
We are pleased to release v1.6.6!
This contains several updated synteny features, including:
Screenshot showing updated import form with ability to load MCScan data
Screenshot showing multiple tracks open at once, with the .anchors (green, gene pairs) and .anchors.simple (black, larger synteny blocks) files from MCScan shown in the dotplot view
Note: MCScan functionality existed internally but was not easy to use. The configuration schema for MCScan anchors files changed also to load the .bed files at startup. See the config guide for details
We also have an updated configuration editor GUI with collapsible sections
Screenshot showing new collapsible (turquoise) sections in the config editor
A number of alignments track look and feel improvements were also added. The scale bar was made to just list the min and max values when the height is small, clip indicator position when horizontally flipped was fixed, and the headroom was removed making the snpcoverage take up the full height of the small area it uses.
There have also been some changes to how internet accounts work. If you use one of the built-in accounts like Google Drive or Dropbox, there's no need to change anything. If you've implemented your own internet account, though, see #2725 for more details.
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.
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jbrowse upgrade to clean up old files
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We are pleased to announce v1.6.5!
This features some various bugfixes to the @jbrowse/cli tool, including better support for large config files with the admin-server, and renaming --out to --root for the admin-server.
It also includes two important fixes related to stats estimation in 1.6.4, one where tracks would display an error on sparse tracks and another where tracks would fail to perform stats estimation on BAM files due to a type confusion.
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.
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This release has a couple long awaited features!
There are also some improvements to synteny and dotplot views. The synteny view can now render curvy lines and "square" the views (so they each have the same zoom level), and have individual search panels in the synteny view. You can now also vertically resize the linear synteny view panel allowing for a taller or shorter view! The rendering has also been sped up in both linear synteny and dotplot views with certain code paths being up to 40x faster.
Also check out the recording and notes from our PAG 2022 tutorial session!
Screenshot showing the new curvy lines of the synteny view with the grape vs
peach demo
http://jbrowse.org/code/jb2/v1.6.4/?config=test_data%2Fconfig_synteny_grape_peach.json&session=share-EdWfJj5aIY&password=S8PGj
note that 1.6.0-1.6.3 were slightly buggy and collected into 1.6.4 here
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.
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This fixes a babel misconfiguration in v1.5.8 that prevented embedded packages from working
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.
This release fixes an important issue where @jbrowse/react-linear-genome-view and other embedded packages did not work with v1.5.5 due to a babel misconfiguration apologies to all affected!
Also we now can access the parent feature in jexl callbacks with parent(feature) or get(feature, 'parent') which is often needed when coloring subfeatures like exon/CDS features
This release also was made because v1.5.6 and v1.5.7 only were half-published to npm, so v1.5.8 fixes it here
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.
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