IGV Team

@riyavsinha @anshulkundaje @arjunmk1 I could try to port your javascript, someone needs to open an issue in the IGV desktop repo though or I will forget. github.com/igv/issues

@anshulkundaje @arjunmk1 @igvteam Unfortunately not! the igv desktop application is a completely different codebase written in Java which I haven't had a chance to get familiar with yet. Would definitely like to support it in the future as well though

Thanks to @riyavsinha in my lab, @igvteam browser will natively support dynseq (dynamic sequence tracks) in an upcoming release. These tracks are very useful to directly visualize base-resolution scores (e.g. contribution scores from ML models, conservation etc). 1/

We now have an IGV tutorial on sandbox.bio! Learn to visualize genomics data and distinguish real variants from artifacts: ➡️ sandbox.bio/tutorials?id=i…

pytor update !! thanks to @igvteam, both igv.js and igv-webapp now support pytor files, making it easier to visualize your data. Check out igv.org/app to try it out using a pytor file. See: github.com/igvteam/igv.js… #igv #pytor #cnvpytor #cnv

IGV 2.16.0 is released with options to color bases from @PacBio alignments by SMRT kinetic values. Thanks to Chris Saunders @ctsa11 for the PR. Details here github.com/igvteam/igv/wi…

Published in Bioinformatics "igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)". doi.org/10.1093/bioinf… #nciitcr #Bioinformatics

@Phil_A_Richmond See reply just tweeted. Open a git issue or use the igv-help forum for further discussion.

@igvteam I mean from a bam file sitting in AWS. Is this still the best widget? umccr.org/blog/igv-amazo…

What's the best way to visualize #genomics data in IGV @igvteam with data residing on AWS S3?

@Phil_A_Richmond For more info see the igv github readme, scroll to bottom: #amazon-web-services-support" target="_blank" rel="nofollow noopener">github.com/igvteam/igv#am…

IGV 2.14.0 is released with a new coloring mode for 5-Methylcytosine modifications. See github.com/igvteam/igv/wi…

igv-reports (pypi.org/project/igv-re…) now supports multi-locus views for structural variants. Example report here: igv.org/igv-reports/ex…. Thanks to @devangvang for this PR.

@gsherloc Very nice. For an alternative approach, which yields "live" views as opposed to screenshots, checkout igv-reports. github.com/igvteam/igv-re…

I love @igvteam’s batch file mode for taking screenshots, so you can curate variants. In this case, I’m examining candidate Ty insertions, and it only takes a few minutes to dump a few hundred images which I can quickly browse through.

Updated IGV url tinyurl.com/ycyfty8c

IGV desktop and igv-webapp have been updated with the #T2T CHM13 v2.0 assembly. Thanks to Maximilian Haeussler and the track hub team(s) at UCSC. tinyurl.com/y9rbppkp

igv-notebook for Colab and Jupyter is now in pypi, "pip install igv-notebook". Example notebook colab.research.google.com/drive/1ebC3QUJ…

igv.js can now be used in Colab notebooks colab.research.google.com/drive/1ebC3QUJ…

IGV Desktop can now interact with an app wrapping the JBrowse Circular View component to explore long range interactions. See github.com/igvteam/igv/wi… for details.

Excited to announce 42basepairs.com, an app to explore your genomics cloud data! Hook up existing S3 buckets, inspect data without downloading it, and collaborate in real-time with multiplayer IGV 🧬 ⛅ Check out the trailer: youtu.be/JaNzjaKJSJk

Attention: If you are running an older version of IGV, versions from 2.4 to 2.11.8 were shipped with log4j2, which is subject to the "Log4shell" vulnerability. We recommend you update IGV to the latest version, 2.11.9, which does not use log4j. tinyurl.com/3ydf33j8

@RobAboukhalil Very cool.

🎮 Multiplayer IGV, anyone? Here's a sneak peek of a prototype I built to enable scientists to collaborate on a shared IGV.js view. It uses WebSockets and Cloudflare Durable Objects to sync state.

igv.js and igv-web (igv.org/app) now support viewing alignments (BAM) and variants (VCF) from htsget servers.