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ยท 2 min read

This adds the ability for users and admins to configure filters to tracks. Users can edit the filters interactively with a "Edit filters" dialog box in the track menu, allowing them to only show features above a certain score, or of a certain type, etc.

Screenshot showing the "Edit filters" dialog, making only a single feature type visible

There is also an important bugfix for the "Show soft clipping" feature of alignments tracks

Downloadsโ€‹

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 v1.22.22 $ lerna-changelog --silent --silent --next-version 2.11.2

2.11.2 (2024-06-03)โ€‹

๐Ÿš€ Enhancementโ€‹

๐Ÿ› Bug Fixโ€‹

Committers: 3โ€‹

ยท 2 min read

This fixes a couple of bugs:

  • fixed inkscape/illustrator compatibility with SVG exports
  • fixed an issue where bookmarks would show up or crash due to loading on the incorrect assembly, and more
  • improved remembering of the state of the collapsed categories in the track selector using localStorage

Screenshot of fixed alpha channel from exported SVGs that improves usage with Inkscape/Adobe Illustrator

Downloadsโ€‹

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 --silent --next-version 2.11.1

2.11.1 (2024-05-11)โ€‹

๐Ÿš€ Enhancementโ€‹

  • core
    • #4354 Allow capitalizing CDS sequences and lowercasing introns in sequence feature panel (@cmdcolin)
  • Other
    • #4351 Store and retrieve user track selector settings in local storage (@cmdcolin)

๐Ÿ› Bug Fixโ€‹

  • core
    • #4381 Replace all rgba(...) color strings with rgb(...) in SVG exports to fix usage in illustrator/inkscape (@cmdcolin)
    • #4364 Fix tooltips creating a scrollbar when overflowing off the screen in Chrome (@cmdcolin)
  • Other
  • app-core

Committers: 1โ€‹

ยท 3 min read

This release adds a new option "Color by CDS" to color the reference sequence track and CDS features in gene tracks by their reading frame

Screenshot showing the "Color by CDS" setting on the linear genome view menu

This release also adds new Hi-C coloring options, including a log-scale mode that enhances visible patterns

There are also many other small fixes including the ability to highlight multiple regions from the URL bar &highlight= option, faster zooming with the zoom in/out buttons, and more

See release notes for details

Downloadsโ€‹

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 --silent --next-version 2.11.0

2.11.0 (2024-04-16)โ€‹

๐Ÿš€ Enhancementโ€‹

๐Ÿ› Bug Fixโ€‹

  • Other
    • #4318 Use node-fetch-native to fix warning from JBrowse CLI on node 21+ (@cmdcolin)
    • #4319 Fix Hi-C rendering for some high resolution files (@cmdcolin)
    • #4314 Fix loading of BED12 data from a plaintext BED with column headers (@cmdcolin)
    • #4293 Fix alignment curves showing up in inkscape for breakpoint svg (@cmdcolin)
    • #4287 Fix snap package and also add deb package (@cmdcolin)
    • #4277 Fix usage of --assemblyNames in jbrowse add-connection (@cmdcolin)
    • #4275 Fixes bug on URL highlight param in which refName aliases were not working (@carolinebridge-oicr)
  • text-indexing

Committers: 3โ€‹

ยท 2 min read

This release adds the ability to highlight regions on the linear genome view.

Users can specify a highlight via the URL when they use jbrowse-web, in a format like &loc=chr1:1-1000&assembly=hg19&highlight=chr1:1-100 (it must be used with the &loc and &assembly)

This release also fixes the ability to load BAM and CRAM files where the refName contains a colon

Downloadsโ€‹

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 --silent --next-version 2.10.3

2.10.3 (2024-03-06)โ€‹

๐Ÿš€ Enhancementโ€‹

๐Ÿ› Bug Fixโ€‹

  • #4254 Throw if no sequenceAdapter supplied to CramAdapter (@cmdcolin)
  • #4250 Fix the viewport calculations for when URL params includes &tracklist=true (@cmdcolin)
  • #4232 Fix for missing INFO.STRANDS tag for TRA features in breakpoint split view (@cmdcolin)
  • #4224 Fix parsing of BAM and CRAM refNames that contain a colon (@cmdcolin)

๐Ÿ“ Documentationโ€‹

Committers: 5โ€‹

ยท 2 min read

Get stack traces from error messagesโ€‹

This release adds a new feature to allow getting the stack trace from error messages, which will show the exact line of code the error occurred on and will help with debugging error reports.

Launch breakpoint split view from alignment feature detailsโ€‹

Previously, you could launch a breakpoint split view from a TRA/breakend type feature in the variant feature details, but this allows you to do it directly via a read

Screenshot showing the workflow to launch a breakpoint split view from a read

@jbrowse/img tool fixesโ€‹

The jb2export command line image exporter from @jbrowse/img had issues with node.js preventing it from running, so this was fixed, and a new ability to export just snpcov visualizations was added. Example

jb2export --bam file.bam snpcov height:400 --fasta hg19.fa --out output.png

Downloadsโ€‹

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 --silent --next-version 2.10.2

2.10.2 (2024-02-19)โ€‹

๐Ÿš€ Enhancementโ€‹

  • Other
    • #4219 Add ability to render only snpcoverage in jbrowse-img (@cmdcolin)
    • #4196 Allow adding &tracklist=true to URL bar to open the track selector, &nav=false to hide linear genome view header (@cmdcolin)
  • core
    • #4215 Launch breakpoint split view directly from alignments feature details (@cmdcolin)
    • #4184 Add ability to get stack trace for error messages in the UI (@cmdcolin)

๐Ÿ› Bug Fixโ€‹

  • Other
    • #4220 Fix hydration error from translocation features in plaintext VCF adapter (@cmdcolin)
    • #4217 Fix breakpoint split view SVG export occasionally having wrong clipping (@cmdcolin)
    • #4213 Fix issue with tagFilter * in alignments track (@cmdcolin)
    • #4208 Fix @jbrowse/img under node environment (@cmdcolin)
    • #4146 Remove --tracks and --view options from set-default-session CLI (@cmdcolin)
  • core
    • #4190 Remove text selection on sequence track with user-select: none (@cmdcolin)
  • core, product-core
    • #4177 Fix session tracks being displayed in the tracklist on @jbrowse/react-linear-genome-view (@cmdcolin)

๐Ÿ“ Documentationโ€‹

Committers: 1โ€‹

ยท One min read

This is a bugfix release, fixing some issues with svg export and faceted track selector. It also enables directional feet to be drawn on breakend style VCF tracks in the linear genome view with the arc display.

Downloadsโ€‹

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 --silent --next-version 2.10.1

2.10.1 (2024-01-09)โ€‹

๐Ÿš€ Enhancementโ€‹

๐Ÿ› Bug Fixโ€‹

  • Other
  • core
    • #4147 Fix bad svg output in v2.10.0 in cases where feature names have angle brackets (@cmdcolin)

๐Ÿ“ Documentationโ€‹

Committers: 2โ€‹

ยท 3 min read

Hello all, as we wrap up the year, we can see that 2023 was a big year for JBrowse 2!

New "Faceted track selector" featureโ€‹

We added a new "Faceted track selector" feature to JBrowse 2, similar to the JBrowse 1 version! This provides a data grid view of your tracks, with multiple levels of filtering capability

New theming features with dark mode supportโ€‹

We added the ability to choose between custom themes, which was specifically beneficial for delivering better dark mode support

SVG export of all view typesโ€‹

SVG export is a highly requested feature, as it enables publication quality exports of the JBrowse 2 visualizations.

This made it so synteny views, dotplot views, breakpoint split view, and circular view were all supported by the SVG export functionality!

Publication of the JBrowse 2 paperโ€‹

We finally published our JBrowse 2 paper! This followed our biorxiv pre-print almost a year earlier https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02914-z

Mac M1/M2 builds for JBrowse Desktopโ€‹

This let's JBrowse Desktop take advantage of speed improvements in Mac M1/M2.

Note: we only realized we weren't publishing the right builds after a user told us that JBrowse Desktop required virtualization!

Moral of the story, feel free to let us know if you run into any problems :)

New @jbrowse/react-app NPM packageโ€‹

The @jbrowse/react-app package enables the NPM installation of the jbrowse-web (which is otherwise deployed as a folder of pre-built js/css/html).

We still envision jbrowse-web to be the typical way that most users deploy the app, but we think the availability of the NPM package is important for certain use cases.

Office hours and community meeting outreach effortโ€‹

In Fall 2023, we created a new effort to do office hours where users can schedule 1-on-1 meetings with the dev team.

We have already conducted

  • 6 1-on-1 office hours meetings
  • 3 community meetings

We met a diverse group of users via these sessions who we had not talked to through other channels like GitHub issues/discussions. We look forward to continuing these meetings through the new year!

New structural variant visualization featuresโ€‹

We have long had the 'circos' view of structural variants, but in 2023 we added 'arc style' rendering of SVs in the normal linear genome view from either "breakend style" VCF, "symbolic style" VCF (<INV>, <DEL>, <DUP>, <CNV>), or BEDPE

Improved synteny scalabilityโ€‹

In v2.10.0, we created a new way to load 'indexed PAF files' that we call PIF files.

This greatly improves the speed and scalability of loading synteny data, since it allows you to load just the alignment data in a region of interest instead of the whole file!

Track selector improvementsโ€‹

We created a new feature for keeping track of your "Recently used tracks" and "Favorite tracks", which we think will be helpful especially for instances with large track lists!

New JBrowseR and jbrowse-jupyter releasesโ€‹

We have renewed our efforts and released new versions of JBrowseR and jbrowse-jupyter.

Notebook style usages of JBrowse 2 with R and Python are very compelling for certain use cases, and we look forward to seeing more usages of this in the new year!

New pluginsโ€‹

This year we introduced a new JBrowse 2 MAFViewer plugin (https://github.com/cmdcolin/jbrowse-plugin-mafviewer), for viewing multiple alignment format files. We have already seen integrations where a Cactus pangenome can be exported into MAF and loaded into the MAFViewer track using workflows from https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/progressive.md#maf

Looking forward!โ€‹

We look forward to the new year, and thank everyone for their support, bug reports, and participation

ยท 3 min read

New file format for synteny tracks - PIFโ€‹

This release adds a new synteny file format PIF ("pairwise indexed format"). It is essentially a small transformation of PAF ("pairwise mapping format") that allows querying the format using tabix.

Preparing a new PIF fileโ€‹

To prepare a PIF file, you can use the @jbrowse/cli tool:

Old workflow

minimap target.fa query.fa > query_vs_target.paf
jbrowse add-assembly target.fa
jbrowse add-assembly query.fa
gzip query_vs_target.paf # optionally gzip paf
jbrowse add-track query_vs_target.paf.gz -a query,target

New

minimap target.fa query.fa > query_vs_target.paf
jbrowse add-assembly target.fa
jbrowse add-assembly query.fa
jbrowse make-pif query_vs_target.paf # generates pif in same folder
jbrowse add-track query_vs_target.pif.gz -a query,target

Conceptually, the PIF file is just a tabix file that allows querying the PAF from either the query->target or the target->query.

Note: We have not yet improved the amount of data needed to view whole-genome overviews of the whole genome alignment, but we anticipate looking into this soon

Impact of using PIF vs PAFโ€‹

This screenshot shows the example impact of loading a synteny track in the linear genome view: the indexed PIF track allows only a small amount of data to be downloaded, and so it is rendered much quicker. The data is exactly the same as a PAF file

Share link for the screenshot above https://jbrowse.org/code/jb2/main/?config=test_data%2Fhs1_vs_mm39%2Fconfig.json&session=share-DMGteXDmT3&password=6TIWA

Other new features in this releaseโ€‹

  • added ability to create highlighted regions from the bookmark widget
  • click-and-drag or wheel side-scroll in the 'synteny area' of the linear synteny view. additionally, right context click on synteny features
  • added support for lzma compression in CRAM files (via @gmod/cram@v2.0.0)

Downloadsโ€‹

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 --silent --next-version 2.10.0

2.10.0 (2023-12-15)โ€‹

๐Ÿš€ Enhancementโ€‹

  • core
    • #4138 Speed up large FromConfigAdapter usages with alternative adapter id calculation (@cmdcolin)
    • #4114 Improve pluginManager.jexl typescript definition (@cmdcolin)
  • Other
    • #4135 Split "recently used tracks" local storage keys by view assemblies (@cmdcolin)
    • #4003 Adds the ability to highlight regions using the bookmarks widget (@carolinebridge-oicr)
    • #4123 Remove session.notify after using the Add track workflow (@cmdcolin)
    • #3859 Add new pairwise indexed PAF adapter format with CLI creation workflow (@cmdcolin)
    • #4109 Allow right clicking synteny features (@cmdcolin)
    • #4110 Scroll both panels of the linear synteny view when side scrolling the middle panel (@cmdcolin)
    • #4108 Convert to floating-ui for tooltips for small speedup (@cmdcolin)
    • #4107 Refactors and bundle size improvements (@cmdcolin)
  • app-core, core
    • #4134 Add ability to click and drag synteny area of synteny view to side scroll (@cmdcolin)

๐Ÿ› Bug Fixโ€‹

  • Other
  • core
    • #4136 Fix "Export SVG" feature in next 14 (@cmdcolin)
    • #4125 Fix internet accounts not being shown in file selector after page refresh and hide HTTP basic internet accounts (@cmdcolin)
  • app-core, embedded-core
    • #4121 Fix view menu checkboxes not responding in some cases (@cmdcolin)

๐Ÿ“ Documentationโ€‹

  • app-core, product-core, web-core

๐Ÿ  Internalโ€‹

Committers: 2โ€‹

ยท 2 min read

This release adds a new feature for keeping track of your "Recently used tracks" and tagging "Favorite tracks" . This will be valuable especially to users and organizations who have large tracklists!

Screenshot showing "Recently used tracks" dropdown menu

We also added the ability to load "single file hubs" from UCSC. These must be manually pasted in the "Add connection" but in the future, we may add ability to auto-load the hubs via the URL bar or similar. You can find a large amount of these single file hubs from GenArk! https://hgdownload.soe.ucsc.edu/hubs/

Finally, this release also fixes an issue people saw with auto-updates for JBrowse Desktop on Mac failing.

Downloadsโ€‹

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 --silent --next-version 2.9.0

2.9.0 (2023-11-30)โ€‹

๐Ÿš€ Enhancementโ€‹

  • Other
    • #4070 Add support for single file hubs (@cmdcolin)
    • #4096 Allow searching by gene name using linear synteny view (@cmdcolin)
    • #4068 Allow searching the text-index by gene name from the URL bar (@cmdcolin)
    • #3948 Make the default setting for the dotplot/synteny views use 'Existing tracks' by default (@cmdcolin)
    • #4039 Adds "Favorites" and "Recently used" track categories to the track selector (@carolinebridge-oicr)
    • #4067 Add arc plugin to @jbrowse/react-linear-genome-view core plugins (@cmdcolin)
  • core, product-core
    • #4091 Allow hiding subfeatures in the feature details panel (@cmdcolin)

๐Ÿ› Bug Fixโ€‹

  • core
  • Other
    • #4095 Fix faceted metadata header names colliding with non-metadata header names (@cmdcolin)
    • #4071 Fix Mac auto-updates fetching non-existent zip (@cmdcolin)
    • #4062 Fix duplicate key error in hierarchical track selector from using connections (@cmdcolin)

Committers: 2โ€‹

ยท 2 min read

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/

Downloadsโ€‹

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)โ€‹

๐Ÿš€ Enhancementโ€‹

  • Other
  • product-core
  • core
    • #4035 Prompt to horizontally flip view when launching linear synteny view on inverted feature (@cmdcolin)
  • app-core

๐Ÿ› Bug Fixโ€‹

  • #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)

๐Ÿ“ Documentationโ€‹

Committers: 2โ€‹