Ensembl is rapidly working towards annotating large collections of genomes based on the nodes of the Earth BioGenome Project. Our aim is to characterise the genome of new species to reinvigorate our understanding of biological diversity, strengthen conservation efforts, and benefit human welfare. Read more to find out how Ensembl will contribute to tackle the climate change challenges that face the world today.
Continue readingCategory: Other news
Additional human variant analysis options in the new Ensembl VEP web interface
The new Ensembl Variant Effect Predictor (Ensembl VEP) web interface now has more extensive options for variants on the human GRCh38 assembly, including allele frequencies, phenotype associations and variant impact scores.
Continue readingEnsembl is moving to our new platform this week
Ensembl is moving to our new platform for genome data and annotation this week. We will begin with the Ensembl Genomes sites and end with the Ensembl 116 site at www.ensembl.org.
The default URL for our new site will be www.ensembl.org. This site offers new scientific opportunities, as genomes and genesets are now available for a diverse array of species from across the tree of life.
Please explore the site and the range of data available, and contact us with your needs, especially regarding new data and working with pangenome data.
There are many new features coming to the new Ensembl, along with the features you have come to love in our legacy sites. If there is a feature you need which is not yet available on the new site, the legacy sites remain available via our archives.
We have a new integrated release on our new site – 2026-07 – which integrates the latest genesets from the Ensembl 116 and Ensembl Genomes 63 releases. Read more.
We also delivered webinars on transition topics, including Educating with Ensembl, the new site, and programmatic access to genome data. Recordings are available.
Thank you for your patience over this transition period, and for joining us as we aim to share more genome data than ever before. We look forward to the insights and discoveries to come.
Updates to FTP site of the new Ensembl website
The FTP site for the new Ensembl website has a new structure. In the updated structure, files are now organised under GCA/ and GCF/ subdirectories, for example: https://ftp.ebi.ac.uk/pub/ensemblorganisms/GCA/. This structure is available for all releases on the site, including the latest partial release 2026-06-07. It will be the standard structure for all subsequent releases.
The structure organised by species name at https://ftp.ebi.ac.uk/pub/ensemblorganisms/ will be retired in August 2026. Please be aware that this change will affect workflows and pipelines pointing to this site. This structure has been maintained for partial release 2026-06-07, and it will remain for three more partial releases in July 2026. We recommend adapting pipelines or workflows to the updated structure as soon as possible.** When it is retired, data will be deleted, and URL links to these will fail.
Continue readingEnsembl MySQL services will be upgraded to MySQL 8 soon
Users of the publicly accessible Ensembl MySQL servers should note that we will soon be upgrading these services from MySQL 5.6 to MySQL 8.
Continue readingExpanded transcript set available in the latest human GRCh38 partial release on the new Ensembl site
In the current Ensembl release (Ensembl 115), the GRCh38 human Ensembl/GENCODE reference annotation was updated to include approximately 121,000 new protein-coding transcripts. This expanded set is based on long-read RNA-seq data processed by the manually supervised automated pipeline TAGENE, which is presented as the source in both browser and files.
The latest partial release for GRCh38 on the new Ensembl (partial release 2026-01-26) includes this new geneset. Some genes and genomic features in this set have several hundred transcripts, such as ZBTB20 (ENSG00000181722) which has 360 transcripts.
Continue readingWhat’s coming in Ensembl release 116 / Ensembl Genomes 63?
Ensembl 116 and Ensembl Genomes 63 are expected in April 2026. Check out what we’re up to, although we can’t guarantee everything listed here will make it into the release.
Special Notice
Ensembl 116 and Ensembl Genomes 63 will be the final releases on the current Ensembl site and platforms.
From the summer of 2026, all new data will only be available through the new Ensembl site. The site, ensembl.org, will redirect to the site currently hosted on beta.ensembl.org.
Continue readingService notice – server issues affecting the Ensembl mirror sites
We are working on server issues affecting the Ensembl mirror sites. A workaround is to use the Ensembl main site via the following link – https://ensembl.org?redirect=no or a recent archive such as https://may2025.archive.ensembl.org/. You can also try the new Ensembl site at https://beta.ensembl.org and let us know about the features you would like to see there.
Updates to programmatic access to Ensembl and transitioning to the new Ensembl Platform
Ensembl is currently undergoing a major transformation to provide faster, more flexible, and more scalable access to genome data. As outlined in our Ensembl 2026 publication, work on the new platform is well underway and can already be explored at beta.ensembl.org. In this blog, we are sharing important information about upcoming changes to Ensembl data access, including timelines, new services, and what you need to do to prepare.
Continue readingChanges to default track visibility in selected Cactus alignment image views
Gene and Sequence tracks in Genomic Alignment Images for selected Cactus alignments will be hidden from view at medium and large scales in Ensembl Release 114.
Continue readingDefault gene track for Human in Ensembl 114 changed to GENCODE Primary
The default track display for Human in Ensembl 114 displays transcripts from the GENCODE Primary set.
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