JBrowse v3.0.0
v3.0.0 Release | JBrowse
Hello all!
jbrowse.org
January 30, 2025 at 7:30 PM
JBrowse v3.0.0
We are pleased to announce JBrowse v3.0.0! This is the latest semver bump to our JBrowse 2 product line
For this release, we created new features for phased and polyploid VCFs. The new phased mode in particular can reveal interesting patterns of inheritance in trio VCFs
jbrowse.org/jb2/blog/202...
For this release, we created new features for phased and polyploid VCFs. The new phased mode in particular can reveal interesting patterns of inheritance in trio VCFs
jbrowse.org/jb2/blog/202...
January 30, 2025 at 2:43 AM
We are pleased to announce JBrowse v3.0.0! This is the latest semver bump to our JBrowse 2 product line
For this release, we created new features for phased and polyploid VCFs. The new phased mode in particular can reveal interesting patterns of inheritance in trio VCFs
jbrowse.org/jb2/blog/202...
For this release, we created new features for phased and polyploid VCFs. The new phased mode in particular can reveal interesting patterns of inheritance in trio VCFs
jbrowse.org/jb2/blog/202...
I'm happy to have contributed to the latest updates of rice genome annotation database.
Paper: academic.oup.com/nar/advance-...
Database (hosted by University of Georgia): rice.uga.edu
Paper: academic.oup.com/nar/advance-...
Database (hosted by University of Georgia): rice.uga.edu
November 19, 2024 at 5:48 PM
I'm happy to have contributed to the latest updates of rice genome annotation database.
Paper: academic.oup.com/nar/advance-...
Database (hosted by University of Georgia): rice.uga.edu
Paper: academic.oup.com/nar/advance-...
Database (hosted by University of Georgia): rice.uga.edu
JBrowse v3.0.2 released jbrowse.org/jb2/blog/202...
February 13, 2025 at 7:37 PM
JBrowse v3.0.2 released jbrowse.org/jb2/blog/202...
We're big fans of the intuitive JBrowse interface with ZFIN integration! Add customized tracks like variants, knockout/knockdown reagents, and mutant lines among others 🐟 Give it a try here: www.alliancegenome.org/jbrowse2/ #SupportMODs
September 8, 2026 at 8:56 AM
We're big fans of the intuitive JBrowse interface with ZFIN integration! Add customized tracks like variants, knockout/knockdown reagents, and mutant lines among others 🐟 Give it a try here: www.alliancegenome.org/jbrowse2/ #SupportMODs
FlyBase is currently undergoing emergency maintenance.
We hope to be back online tomorrow.
In the meantime, a subset of FlyBase data can be accessed at the Alliance of Genome Resources www.alliancegenome.org, including BLAST and JBrowse services.
We hope to be back online tomorrow.
In the meantime, a subset of FlyBase data can be accessed at the Alliance of Genome Resources www.alliancegenome.org, including BLAST and JBrowse services.
Alliance of Genome Resources
www.alliancegenome.org
September 9, 2026 at 3:25 AM
FlyBase is currently undergoing emergency maintenance.
We hope to be back online tomorrow.
In the meantime, a subset of FlyBase data can be accessed at the Alliance of Genome Resources www.alliancegenome.org, including BLAST and JBrowse services.
We hope to be back online tomorrow.
In the meantime, a subset of FlyBase data can be accessed at the Alliance of Genome Resources www.alliancegenome.org, including BLAST and JBrowse services.
We are continuing on work to bring FlyBase fully back online.
Many more search tools and features are now functioning. JBrowse is back.
BLAST is still down, but available at alliancegenome.org.
Many more search tools and features are now functioning. JBrowse is back.
BLAST is still down, but available at alliancegenome.org.
We are back up. Report pages and basic search function are now available, but some tools are still offline.
FlyBase is currently undergoing emergency maintenance.
We hope to be back online tomorrow.
In the meantime, a subset of FlyBase data can be accessed at the Alliance of Genome Resources www.alliancegenome.org, including BLAST and JBrowse services.
We hope to be back online tomorrow.
In the meantime, a subset of FlyBase data can be accessed at the Alliance of Genome Resources www.alliancegenome.org, including BLAST and JBrowse services.
September 10, 2026 at 2:42 PM
We are continuing on work to bring FlyBase fully back online.
Many more search tools and features are now functioning. JBrowse is back.
BLAST is still down, but available at alliancegenome.org.
Many more search tools and features are now functioning. JBrowse is back.
BLAST is still down, but available at alliancegenome.org.
💻 Variant Calling Project Announcement! 🧬
Will explore the impact of novel operons on Pseudomonas aeruginosa PA14 by analyzing mutations introduced in two mutants compared to the parental strain🔬
I’ll use Snippy for calling & Jbrowse to visualize on Galaxy!
Stay Tuned! 🚀
#Bioinformatics #Genomics
Will explore the impact of novel operons on Pseudomonas aeruginosa PA14 by analyzing mutations introduced in two mutants compared to the parental strain🔬
I’ll use Snippy for calling & Jbrowse to visualize on Galaxy!
Stay Tuned! 🚀
#Bioinformatics #Genomics
January 15, 2025 at 2:35 PM
💻 Variant Calling Project Announcement! 🧬
Will explore the impact of novel operons on Pseudomonas aeruginosa PA14 by analyzing mutations introduced in two mutants compared to the parental strain🔬
I’ll use Snippy for calling & Jbrowse to visualize on Galaxy!
Stay Tuned! 🚀
#Bioinformatics #Genomics
Will explore the impact of novel operons on Pseudomonas aeruginosa PA14 by analyzing mutations introduced in two mutants compared to the parental strain🔬
I’ll use Snippy for calling & Jbrowse to visualize on Galaxy!
Stay Tuned! 🚀
#Bioinformatics #Genomics
The soybean cyst nematode genomics database has been updated as of last night. SCNBase.org now has all 9 early release H. glycines genomes and annotations. All files are downloadable and accessible through BLAST, feature search, and Jbrowse. The pan-genome paper is coming soon! #science #genomics
SCNBase
SCNBase.org
November 27, 2024 at 6:08 PM
The soybean cyst nematode genomics database has been updated as of last night. SCNBase.org now has all 9 early release H. glycines genomes and annotations. All files are downloadable and accessible through BLAST, feature search, and Jbrowse. The pan-genome paper is coming soon! #science #genomics
We’ve also released the Capitella Genome Project Portal, integrating genome annotation with RNA-seq, ATAC-seq & mitochondrial data, along with an interactive JBrowse genome browser and custom BLAST interface. @abhinavsur.bsky.social @kguynes.bsky.social @neva-meyer.bsky.social @chemamd.bsky.social
March 12, 2026 at 4:21 PM
We’ve also released the Capitella Genome Project Portal, integrating genome annotation with RNA-seq, ATAC-seq & mitochondrial data, along with an interactive JBrowse genome browser and custom BLAST interface. @abhinavsur.bsky.social @kguynes.bsky.social @neva-meyer.bsky.social @chemamd.bsky.social
There is no more Flybase mirror in Europe? Any place that can be used to blast Drosophila genome with JBrowse feature?
November 28, 2025 at 6:34 PM
There is no more Flybase mirror in Europe? Any place that can be used to blast Drosophila genome with JBrowse feature?
The Genomic Variant Information section of Allele pages, & the HT Variant page summaries, now display the relevant genome assembly, thousand comma separators for genomic coordinates (for ease of reading, e.g. 3L:20,992,839 not 3L:20992839), & symbol hyperlinks to JBrowse for the respective variant.
![Alliance Allele page for the Drosophila allele skd[T13].
The Genome Assembly (highlighted in pink) is R6.
The genomic location is 3L:21,005,570 (highlighted in blue); that number uses 'thousand comma separators' to make it more easily readable.
The variant symbol (highlighted in orange) hyperlinks to its JBrowse location (circled in orange in the JBrowse image).](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:odqq6j75nbclikfbcf6eoeks/bafkreifpryevcnchuavozbx4najqsfi5kzwpdgrja2jtywlpzpl4jwfhwa)
![The genomic location of the variant associated with the Drosophila allele skld[T13], hyperlinked from the Genomic Variant section of the Allele page. The variant is circled in orange.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:odqq6j75nbclikfbcf6eoeks/bafkreibi73rlyjsx3uijoltg7uazhpz44745i7t3qtfelvxdkdy2hf52sa)
May 14, 2026 at 11:37 PM
The Genomic Variant Information section of Allele pages, & the HT Variant page summaries, now display the relevant genome assembly, thousand comma separators for genomic coordinates (for ease of reading, e.g. 3L:20,992,839 not 3L:20992839), & symbol hyperlinks to JBrowse for the respective variant.
🧬 Looking for #yeast 5'- and 3'-UTR data? Three ways to access:
✅ Bulk downloads sgd-archive.yeastgenome.org/sequence/S28...
✅ #AllianceMine queries www.alliancegenome.org/bluegenes/al...
✅ #JBrowse genome browser jbrowse.yeastgenome.org
Read more at SGD: www.yeastgenome.org/blog/how-to-...
✅ Bulk downloads sgd-archive.yeastgenome.org/sequence/S28...
✅ #AllianceMine queries www.alliancegenome.org/bluegenes/al...
✅ #JBrowse genome browser jbrowse.yeastgenome.org
Read more at SGD: www.yeastgenome.org/blog/how-to-...
How to Find UTR Lengths for Yeast Genes | SGD
The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae.
www.yeastgenome.org
May 21, 2026 at 10:23 PM
🧬 Looking for #yeast 5'- and 3'-UTR data? Three ways to access:
✅ Bulk downloads sgd-archive.yeastgenome.org/sequence/S28...
✅ #AllianceMine queries www.alliancegenome.org/bluegenes/al...
✅ #JBrowse genome browser jbrowse.yeastgenome.org
Read more at SGD: www.yeastgenome.org/blog/how-to-...
✅ Bulk downloads sgd-archive.yeastgenome.org/sequence/S28...
✅ #AllianceMine queries www.alliancegenome.org/bluegenes/al...
✅ #JBrowse genome browser jbrowse.yeastgenome.org
Read more at SGD: www.yeastgenome.org/blog/how-to-...
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, with detailed mouseover information and genotype frequencies in the sidebar
Release notes: jbrowse.org/jb2/blog/202...
Users can now see complex patterns of structural variation from multi-sample VCF files, with detailed mouseover information and genotype frequencies in the sidebar
Release notes: jbrowse.org/jb2/blog/202...
April 18, 2025 at 6:51 PM
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, with detailed mouseover information and genotype frequencies in the sidebar
Release notes: jbrowse.org/jb2/blog/202...
Users can now see complex patterns of structural variation from multi-sample VCF files, with detailed mouseover information and genotype frequencies in the sidebar
Release notes: jbrowse.org/jb2/blog/202...
Apollo 3 wouldn't be possible without JBrowse 2 and its first-rate genome browsing capabilities. Now you can use all of JBrowse 2's features, such as comparative genomics visualizations, in your annotation workflow.
jbrowse.org/jb2/
jbrowse.org/jb2/
JBrowse | JBrowse
jbrowse.org
December 20, 2024 at 4:46 AM
Apollo 3 wouldn't be possible without JBrowse 2 and its first-rate genome browsing capabilities. Now you can use all of JBrowse 2's features, such as comparative genomics visualizations, in your annotation workflow.
jbrowse.org/jb2/
jbrowse.org/jb2/
You can embed Jbrowse in another website, but might be overkill depending on what you want to do with it: jbrowse.org/docs/embeddi...
Embedding JBrowse · JBrowse 1
## Embedding in an iframe
jbrowse.org
November 24, 2024 at 9:41 PM
You can embed Jbrowse in another website, but might be overkill depending on what you want to do with it: jbrowse.org/docs/embeddi...
🌱🧬PMGD is the first specialized database for plant mitochondrial genomes, housing 1,829 genomes from 1,307 species with built-in BLAST, JBrowse & phylogeny tools
A user-friendly platform for plant evolution & diversity research #plantscience @jipb.bsky.social onlinelibrary.wiley.com/doi/10.1111/...
A user-friendly platform for plant evolution & diversity research #plantscience @jipb.bsky.social onlinelibrary.wiley.com/doi/10.1111/...
PMGD: A comprehensive database of plant mitochondrial genomes
PMGD is the first specialized database for plant mitochondrial genomes. Housing 1,829 genomes from 1,307 species across five major plant lineages, it provides standardized high-quality data and built...
onlinelibrary.wiley.com
July 30, 2026 at 10:00 AM
🌱🧬PMGD is the first specialized database for plant mitochondrial genomes, housing 1,829 genomes from 1,307 species with built-in BLAST, JBrowse & phylogeny tools
A user-friendly platform for plant evolution & diversity research #plantscience @jipb.bsky.social onlinelibrary.wiley.com/doi/10.1111/...
A user-friendly platform for plant evolution & diversity research #plantscience @jipb.bsky.social onlinelibrary.wiley.com/doi/10.1111/...
Excited to share this demo of using AlphaGenome in JBrowse 2!
July 9, 2025 at 2:14 PM
Excited to share this demo of using AlphaGenome in JBrowse 2!
For those passionate about the aphid: Dysaphis plantagina, the #REPET track is now available on BIPAA JBrowse (bipaa.genouest.org/sp/dysaphis_...) with a direct link to #RepetDB for each #transposon copy! Enjoy! #TEsky
JBrowse
bipaa.genouest.org
December 18, 2025 at 9:54 AM
For those passionate about the aphid: Dysaphis plantagina, the #REPET track is now available on BIPAA JBrowse (bipaa.genouest.org/sp/dysaphis_...) with a direct link to #RepetDB for each #transposon copy! Enjoy! #TEsky
JBrowse (JaminGames©, 2010-01-12)
This is a small web browser with a nice skin. It's based on Internet Explorer so it should run just about any web app out there.
Feel free to use in your games just give me the credit.
This is a small web browser with a nice skin. It's based on Internet Explorer so it should run just about any web app out there.
Feel free to use in your games just give me the credit.
August 13, 2026 at 5:16 PM
JBrowse (JaminGames©, 2010-01-12)
This is a small web browser with a nice skin. It's based on Internet Explorer so it should run just about any web app out there.
Feel free to use in your games just give me the credit.
This is a small web browser with a nice skin. It's based on Internet Explorer so it should run just about any web app out there.
Feel free to use in your games just give me the credit.
This features assemblies end-to-end, and includes variant coordinates, VEP transcript annotations, sequence panels, and JBrowse tracks.
September 7, 2026 at 11:42 PM
This features assemblies end-to-end, and includes variant coordinates, VEP transcript annotations, sequence panels, and JBrowse tracks.