This release fixes the UMD builds for the react components which failed to upload to npm in 2.1.3
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 includes a quality-of-life improvement for users plotting synteny with CIGAR strings. Before this version, the x-axis in the dotplot was assumed to be target sequence (and similarly, the top row in the linear synteny view was assumed to be the target sequence). But now, target can be either x- or y-axis in dotplot, and top or bottom in linear synteny views, removing the need for the user to care as much about query-vs-target ordering.
This release also includes several fixes for the the behavior of text searching in the linear genome view, a new button to open a .jbrowse file directly from the start screen on jbrowse-desktop, and an important bugfix to plotting inverted alignments on dotplots that affected versions v2.1.0-v2.1.2.
Screenshot showing the latest jbrowse desktop start screen, with a button to open .jbrowse sessions
Screenshot showing both X/Y orientations of two yeast genomes on the dotplot view, focusing on the deletions and insertions.
Enjoy!
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.
core
core
core
Hello all, we are pleased to announce v2.1.2!
This release includes a number of small bugfixes to the multi-wiggle track type, and a new feature for performing small sequence searches/motifs in the visible region.
Screenshot of the sequence search feature. It is available from the "view menu" on the linear genome view
Also, we just recently published the pre-print for our JBrowse 2 paper on bioRxiv! https://www.biorxiv.org/content/10.1101/2022.07.28.501447v1
This is a tour de force describing the basic ideas behind JBrowse 2 as an app. We are really pleased with how users and developers have helped to contribute to JBrowse 2 thus far, and look forward to many more years!
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.
core
core
We are pleased to present 2.1.0! This release adds some significant new features including:
Example links for multi-bigwig sessions
ENCODE bigWigs https://jbrowse.org/code/jb2/v2.1.0/?config=test_data%2Fconfig_demo.json&session=share-Pw7kOjagSF&password=e0SuE
COLO829 Tumor vs Normal coverage bigWigs https://jbrowse.org/code/jb2/v2.1.0/?config=test_data%2Fconfig_demo.json&session=share-J4owOIkT0F&password=orr2h
Multi-row plot showing 21 ENCODE bigWig tracks
Overlapping "xyplot" rendering multiwiggle rendering mode with "emphasised" points showing tumor vs normal coverage
Dotplot view showing warnings from rendering dotplot, generally due to the wrong assemblies being compared. Screenshot also shows the dropdown menu to choose whether mouse click-and-drag pans the view or selects a region
Undo and redo buttons in the Tools menu, also accessible from keyboard shortcuts ctrl+z/ctrl+y and cmd+z/cmd+shift+z. The Undo/Redo function is available in jbrowse-web and jbrowse-desktop currently
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.
core
core
We are pleased to announce 2.0.1
This release features the ability to mouseover and click synteny alignments on the linear synteny view
If there are base level alignments, either from the read vs ref view or e.g. a PAF file generated with minimap -c (outputs CIGAR), then you can also mouse over to get information about the particular part of that alignment e.g. the CIGAR string
Figure showing a mouseover inside a deletion in the read vs ref view
This release also has some other small fixes and improvements, see release notes!
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.
core
core
We are pleased to release v2.0.0! This is a major version milestone, but it does not have a huge number of changes. Instead, the major change that resulted in becoming v2.0.0 was the upgrade of many of our dependencies including
Therefore, to help users that may have been relying on library versions like this, it is safer to make the version a major bump. If you run into any issues with this upgrade, let us know and we can help
Some notable improvements:
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.
text-indexing
__mocks__, core, text-indexing
core
We are excited to announce v1.7.11!
This release has some relatively small fixes to the UI, docs, and examples. For
developers, they may notice that we have removed node-canvas due to it's need
for having extra system dependencies, and because it only really was needed in
niche circumstances. This will improve the ease of installing packages like
@jbrowse/react-linear-genome-view.
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.
core
We are pleased to present the latest JBrowse 2 release!
This has some great new features including
Here is an example which adds a link to the "Name" panel in the feature details. It uses the jexl callback that returns an object with keys for each field to modify (e.g. the key name is used here). See
{
"type": "FeatureTrack",
"trackId": "ncbi_gff_hg19_2",
"name": "NCBI RefSeq",
"formatDetails": {
"feature": "jexl:{name:'<a href=https://google.com/?q='+feature.name+'>'+feature.name+'</a>'}"
},
"assemblyNames": ["hg19"],
"adapter": {
"type": "Gff3TabixAdapter",
"gffGzLocation": {
"uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz"
},
"index": {
"location": {
"uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz.tbi"
}
}
}
}
Example screenshot
See https://jbrowse.org/jb2/docs/config_guide/#customizing-feature-details-panels for more info
Before
After
See also the "Copy config" button to download the config
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.
core
__mocks__, core
core
We are pleased to present v1.7.9!
This release features several bugfixes and improvements submitted by community members, including a CLI fix when specifying --indexFile with CSI files, and a new feature to get FASTA metadata from an external file.
Additionally, we have switched to canvas2svg for SVG exports, which can now handle more sophisticated operations like bezierCurves (used for sashimi-style arc in RNA-seq data), and circles (used by jbrowse-plugin-gwas)
Before (note bad intron and lack of arcs rendered on bottom track)
After (fixed intron rendering and arcs)
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.
core
core
We are happy to announce v1.7.8
Some highlights include
Screenshots showing the new viewing of indels when viewing methylation
Before
After
See the release notes for 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.