I am very pleased to announce the release of JBrowse version 1.16.0!
A major new feature of this release is the introduction of paired read visualization options!
And rather than delivering just one type of paired read visualization, there are many options for this including:
- Pileup - standard alignments view but with connections between pairs
- Read cloud - plotting by insert size
- Arc view - plotting paired reads as connected arcs
There are also multiple coloring options for each type of view, including coloring by insert size (so abnormally large inserts are colored red for example) or pair orientation. Here are some example screenshots to help demonstrate
Figure 1.standard pileup view with paired and unpaired modes on the same data.
Figure 2. arc view which shows many long-range connections from a mate pair dataset.
Figure 3. The read cloud view showing color by orientation and size (red being abnormally large insert size, and turquoise and blue being incorrect pair orientations)
JBrowse version 1.16.0 also contains many other features and bug fixes, so please review the changelog below! Also make sure to view the paired read documentation for more information on the paired read options.
- JBrowse-1.16.0.zip - minified release
- JBrowse-1.16.0-dev.zip - use this if you modify jbrowse source code or use plugins
- Added ability to view paired read data as connected entities for BAM and CRAM store classes. There are multiple different viewing options for this including plotting by insert size, plotting as connected arcs, or pileup views for the paired reads. Additonally multiple color schemes are available for coloring by insert size, pair orientation, mapping quality, and more. Thanks to @garrettjstevens, @rbuels, @AndyMenzies, and @keiranmraine for testing. Also a big thanks to @jrobinso from @igvteam for contributions to CRAM code related to paired reads (issue #1235, @cmdcolin)
Created new BAM parsing mechanism using the npm module @gmod/bam. Users might see some modest performance improvements due to enhanced tooling. Thanks to @rbuels and others for testing and feedback (issue #1215, issue #1178, @cmdcolin)
Add support for generate-names to index VCF features that have multiple IDs in the ID column (@cmdcolin)
Improved error message that is displayed when a data file cannot be fetched via CORS (@rbuels)
Added a --bgzip_fasta option for prepare-refseqs.pl and also the ability to index reference sequence names if they are manually specified as a fasta index e.g.
refSeqs=genome.fai. Thanks to @FredericBGA for the report! (issue #1281, issue #1282, @cmdcolin).
Fixed issue where some feature mouseovers where not working properly (issue #1236, @cmdcolin)
Fixed issue where JBrowse would load the wrong area of the refseq on startup resulting in bad layouts and excessive data fetches. Thanks to @hkmoon, @cmdcolin, and @garrettjstevens for debugging (issue #1190, issue #1235, pull #1187)
Fixed issue where some parts of a CRAM file would not be displayed in JBrowse due to a CRAM index parsing issue (@cmdcolin)
Fixed an issue where BAM features were not lazily evaluating their tags (@cmdcolin)