JBrowse
JBrowse boosted:
Alliance of Genome ResourcesAllianceGenome@genomic.social
2025-05-09

This month's Alliance webinar is 'JBrowse2 at the Alliance', presented by Jeff De Pons with co-host Anne Kwitek, on Thursday May 15 at noon EDT. Please preregister by Wednesday May 14 (by midnight EDT please) to get the Zoom link forms.gle/GzMnmwK23SzPxbQw7
You can find the schedule of upcoming Alliance Office Hours, as well as links to the recordings of previous webinars on the Alliance Event Calendar alliancegenome.org/event-calen

2025-04-18

JBrowse v3.3.0 is released, featuring a big update: multi-sample SV visualization!

Users can now see complex patterns of structural variation from multi-sample VCF files. Users can also get detailed mouseover information for each sample, and see genotype frequencies in the sidebar

Release notes: jbrowse.org/jb2/blog/2025/04/1

screenshot of 3202 human genome samples showing the structural variant visualizer in jbrowse
JBrowse boosted:
2025-03-18

trying out the 1001 genomes data (arabidopsis) with the multi-sample variant viewer...

showing some big blocks of "no call" variants (the ./. in VCF ) in yellow...sort of indirect but these are a great 'secondary' signal for deletion SVs

JBrowse boosted:
2025-03-05

finally made a little breakthrough on finding "phased segments" from a phased VCF...had to twiddle with the hap-ibd settings to lower the defaults to output much smaller blocks. these are fragmented, but do correspond to valid blocks from what i can tell

picture shows the correspondence between hap-ibd output and the raw VCF data with a trio VCF (6 rows, each row being a haplotype of the sample)

2025-03-05

Apollo 2.8.0 released with an important security patch

github.com/GMOD/Apollo/release

2025-02-13

I know it's a bit late, but we finally got around to writing our 2024 year in review! jbrowse.org/jb2/blog/2025/02/1

Let us know what you think!

2025-01-30

For those of you who are on BlueSky, we also just kicked off our BlueSky account. Give us a like and a follow :) bsky.app/profile/jbrowse.org

2025-01-30

JBrowse v3.0.0 released! You can keep calling it JBrowse 2, we just did the major version bump to be good semantic versioning citizens (JBrowse 2 itself has already gone from 0.0.1->1.x.x->2.x.x->now 3.x.x)

In this release we added new phased VCF and polyploid VCF visualizations and a bunch more

Release notes here jbrowse.org/jb2/blog/2025/01/2

2024-12-11

JBrowse v2.18.0 released, with new "matrix" view of variants, redesigned SV inspector, easier access to autosaved sessions, optimized GWAS view, and more! jbrowse.org/jb2/blog/2024/12/1

2024-11-19

JBrowse v2.17.0 also just released with new improvements for showing base modifications and bedMethyl format, new synteny data adapter types for BLAST output, and more! jbrowse.org/jb2/blog/2024/11/1

2024-11-19

JBrowse v2.16.0 released with the ability to show multi-way synteny! jbrowse.org/jb2/blog/2024/10/2 (released a month ago, but just getting around to posting it)

2024-09-13

JBrowse v2.15.1 released, with some cool new features for visualizing inversions for both paired-end and split-long reads jbrowse.org/jb2/blog/2024/09/1

2024-08-28

JBrowse v2.14.0 is now out, with some cool new features including

- Ability to group alignment track reads by specific tags
- Ability to make a FASTA file with names like e.g. NC_000001.1 to display in the UI as chr1

and more! see jbrowse.org/jb2/blog/2024/08/2 for notes

2024-06-20

The new version also groups multiple transcripts into a gene-level feature in BigBed files automatically

2024-06-20

In this new release, users can see genomic or feature-relative coordinates in the feature details (and pop out the side drawers into a wider screen dialog box! as pictured below)

2024-06-20

JBrowse v2.12.0 released, with a lot of nice little features, and quality of life improvements! See jbrowse.org/jb2/blog/2024/06/2

2024-06-03

JBrowse v2.11.2 released, with a new feature to allow users to interactively add filters to features on genome browser tracks jbrowse.org/jb2/blog/2024/06/0

2024-04-16

We just released JBrowse v2.11.0 with new "Color by CDS" to help see which translation frame is used in the gene glyphs, and new Hi-C "color schemes" and log-transformed display jbrowse.org/jb2/blog/2024/04/1

image of a Hi-C contact matrix in the jbrowse genome browser with a fiery or "fall" like color schemeimage of the "Color by CDS" feature in the jbrowse genome browser showing a gene structure colored purple, with the reference sequence showing protein letters from the third translation frame also colored purple

Client Info

Server: https://mastodon.social
Version: 2025.04
Repository: https://github.com/cyevgeniy/lmst