This release improves support for BEDPE and arc rendering of structural variants.
It also adds a new CLI command called jbrowse sort-gff that intends to help
simplify the loading of GFF tabix tracks.
Usage:
jbrowse sort-gff yourfile.gff | bgzip > yourfile.sorted.gff.gz
tabix yourfile.sorted.gff.gz
jbrowse add-track yourfile.sorted.gff.gz --load copy --out /var/www/html/jbrowse2
The jbrowse CLI tool can load BEDPE files with simply
jbrowse add-track yourfile.bedpe (or, optionally gzipped e.g.
yourfile.bedpe.gz)
Screenshot showing the same data rendered as both a BEDPE file and VCF file with
different variant types (<DUP>, <DEL>, <INV>, <TRA>). Notably, this arc
rendering can render 'cross-region' or 'inter-chromosomal' arcs.
Also, if you haven't seen it, check out our new office hours and community call schedule! See https://jbrowse.org/jb2/blog/2023/11/03/office-hours/
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 v1.22.19 $ lerna-changelog --silent --next-version 2.8.0
2.8.0 (2023-11-09)
🚀 Enhancement
- Other
- #4045 Create multi-region arc display type for variant tracks (@cmdcolin)
- #4050 Allow specifying alternative config.json path via global variable (@cmdcolin)
- #4046 Show last autosave on jbrowse-web start screen (@cmdcolin)
- #4044 Speed up "multi-region" navigation in search box (@cmdcolin)
- #4032 Add
jbrowse sort-gffsubcommand (@cmdcolin)
product-corecoreapp-core- #4024 Add right-handed arrow to view title to emphasize the focused view (@carolinebridge-oicr)
🐛 Bug Fix
- #4052 Fix browser back button behavior in jbrowse-web (@cmdcolin)
- #4043 Fix crash in "Open session" widget for sessions that have 'track-less views' (@cmdcolin)
📝 Documentation
Committers: 2
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin) Done in 2.23s.