v2.8.0 Release

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#

• v2.8.0

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.

2.8.0 (2023-11-09)#

:rocket: 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-gff subcommand (@cmdcolin)
• product-core
  • #4040 Strip baseUri in 'About track' copy config (@cmdcolin)
• core
  • #4035 Prompt to horizontally flip view when launching linear synteny view on inverted feature (@cmdcolin)
• app-core
  • #4024 Add right-handed arrow to view title to emphasize the focused view (@carolinebridge-oicr)

:bug: 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)

:memo: Documentation#

• #4027 Add office hours and community meetings (@cmdcolin)

Committers: 2#

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)