#jbrowse2 — Public Fediverse posts

On Day 2 of European Galaxy Days, Anthony Bretaudeau presented 'Modern genome browsing in Galaxy with Jbrowse2'.
Read more: https://usegalaxy.eu/root?tool_id=jbrowse2

@abretaud @galaxyfreiburg
#genomics #jbrowse2 #EGD2025 #genome #galaxyproject #eosc #fair #genome_browsing #open_science

2/3 along side any other data in #JBrowse2, either provided by the hosting site or loaded by the user. I have an example of what it would look like here: https://test.d2jjb0xowet5mr.amplifyapp.com/?session=share-wsg_ds7a0b&password=hZsD4 where you can see the manhattan plot for the whole genome, and if you zoom in on a peak, you’d see the Curated Genes track too. This example JBrowse isn’t ready for release yet

I posted this question in the C. elegans slack, but I thought I'd ask here to a different (wider but probably sparser) audience: I went to a non-worm genomics conference this week and was struck by how much #GWAS data was being presented. I’m wondering if the same trend is occurring in your research, and if so, if researchers would be interested in our adding functionality to our #JBrowse2 instance that would allow users to view (while not uploading to anywhere) GWAS data ... 1/3

#JBrowse2 workshop about to start at #pag31 in town and country D. Get some updates and a hands on tutorial for setting up your own JBrowse 2!

Gearing up for the #JBrowse2 workshop at #PAG31. We'll be in Town and Country D (used to be called the California room) on Sunday, Jan 14, 1:30 PM to talk about JBrowse 2 and Apollo 3, and run a hands-on workshop on installing and configuring your own JBrowse 2 instance. I hope to see you there! https://plan.core-apps.com/pag_2024/event/0121205505a9f11e6727dfd2f4a4a067

I got up pretty early to watch the WormBase workshop at #worm23 (the international c. elegans meeting) but they aren't streaming any of the workshops 😢
I can at least post a link to a video of my section of the workshop, an intro to #jbrowse2 at #WormBase: https://youtu.be/8IBOotP48Dw

Are there #celegans #worm researchers on mastodon? I'm curious about whether I should spend development time creating a plugin for #jbrowse2 to search for DNA motifs that is similar to the search in JBrowse 1. It would be a non-trivial undertaking. #worm23

I've had a busy week writing. For people who are interested in C. elegans and use http://wormbase.org/, or are more general #JBrowse2 users, I've written several user-focused help documents at the WormBase blog: https://blog.wormbase.org/tags/jbrowse2/

Topics covered include:
*adding your own data
*working with synteny data
*working with lists, bookmarks and sessions
*searching for seqs and features
*getting sequence

Let me know if there are other topics that might be of interest.

@EpicBear @ianholmes Ooh, that is pretty! Nice use of color. Yes, I think #JBrowse2 has a lot to offer.

@thebiologistisn I was thinking about the comparison of 2 similar assemblies and came up with a potentially useful visualization. As a test set I used the C. elegans N2 assembly (original) and the VC2010 assembly (a resequencing of the same strain, so it should be very similar). I already compared these 2 with #minimap2 and have that data on #WormBase's #JBrowse2. I wrote a simple script that would take a sorted paf file (minimap2) and find gaps. This is the result: https://wormbase.org/tools/genome/jbrowse2/?session=share-SSR4hA6gzo&password=TFpjE

@thebiologistisn oh, well, I’m not an expert on comparative genomics, but I do like #minimap2, mostly because it’s easy, fast and gives reasonable looking results for C. elegans and friends. And, not surprisingly, makes nice looking pictures in #JBrowse2 When I get back to my laptop, I’ll post some pictures (still don’t do much genome browsing on my phone :-)

I'm very pleased with myself for getting my first package out on NPM: generic-sequence-panel, which is a React component that displays color annotated fasta sequence. It is a wrapper around code from #JBrowse2 that pulls data from a JBrowse dataset to display it.

The monorepo with a link to a simple example app is on GitHub: https://github.com/scottcain/seqpanel and the package is on npm: https://www.npmjs.com/package/generic-sequence-panel

#JBrowse2 has been a long time coming - seven years in development, ten if you count the first rumblings from Rob Buels. The payoff is an amazingly versatile, fast, and beautiful suite of programs for visualizing general genome annotations, relationships between genomes, and genomic evidence: https://rdcu.be/c98wf

#JBrowse #GenomeBrowser #Genomics #Bioinformatics #GenomeAnnotation #Genome #Genomes

I am very happy to announce that the #JBrowse2 paper has be published in Genome Biology. There is lots of cool stuff in here: synenty, structural variation, plugins, multi chromosome and multi genome views, a graphical configuration editor, a desktop app, and easy-to-embed app.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02914-z

The combination of #JBrowse2 and #AWS is pretty great: during a worm call today, somebody mentioned a genome related to elegans, so (during the call), I spun up an EC2 instance, did a minimap2 comparison between the two genomes, loaded the result in a local JB2 instance to check, then committed a config change to the stage branch, which got picked up by AWS Amplify, and 30 min into the call, I posted a link to the new comparison: https://staging.wormbase.org/tools/genome/jbrowse2/?session=share-mollwNOrzu&password=VSvit

@jogoodma Yeah, #WormBase 's GBrowse is going away at the end of January as well. It's been a heck of a workhorse and can go out to pasture now. Time to move on to #JBrowse2 https://jbrowse.org/ !