by ·Comments Off on Ensembl 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.

by ·Comments Off on Changes to URLs for the new Ensembl site

As part of our transition to the new Ensembl, we have updated the URLs for genomes on our new site. The URLs for integrated genomes now contain genome assembly accession numbers e.g. GCA_000001405.29. Some genomes on our new site contained a genome tag e.g. grch38 (examples in the post below). Saved links to these tags will now fail.

Users actively using the new site should note that any selected genome will need to be reselected after the transition of the beta.ensembl.org URL to ensembl.org. We expect this change in mid-August 2026.

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by ·Comments Off on Feature profile between new and legacy Ensembl – July 2026 update

The new Ensembl site provides broader availability of species and genomes, but as it is in active development, not all the features from the legacy Ensembl (Ensembl 116 and Ensembl Genomes 63) versions are available. Here is a list of features profiled between the versions to help you choose which resource to use. These are valid as of July 2026.

Ensembl sites and data remain available via Ensembl Archives, please use whichever resource meets your needs best.

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by ·Comments Off on Apps renamed on the new Ensembl site

We have renamed the Species selector and Entity viewer apps on the new Ensembl site!

The Entity viewer has been renamed to Feature Explorer:

https://beta.ensembl.org/feature-explorer

The Species selector has been renamed to Genome selector:

https://beta.ensembl.org/genome-selector

To preserve existing links you have saved, the previous URLs for these apps will resolve to the new name based addresses above.

For any questions or issue, please contact the Ensembl Helpdesk.

by ·Comments Off on 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. 

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by ·Comments Off on Ensembl for Educators: a practical resource for teaching Ensembl

We’re pleased to announce our new resource Ensembl for Educators! This resource brings together practical teaching materials, walkthroughs, and support to help educators keep pace with a browser that is updated regularly. Designed to make teaching easier, it gives instructors a central place to find resources they can use, adapt, and reuse in their own teaching. This first edition of Ensembl for Educators contains content and materials for the latest Ensembl version – Ensembl 116/Ensembl Genomes 63.

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by ·Comments Off on Ensembl 116 and Ensembl Genomes 63 have been released!

Ensembl 116 and Ensembl Genomes 63 are here! Highlights include new pig & cattle assemblies, 26 oat genomes, updated alignments and new Ensembl VEP plugins.

Special Notice – Ensembl Transition

Ensembl 116 and Ensembl Genomes 63 are the final releases on the current Ensembl site and platforms. 

All new data from this point will only be available through the new Ensembl site. In the next few months, the ensembl.org site will bring you to the site hosted on beta.ensembl.org. 

You will continue to have access to current Ensembl versions via Ensembl Archives, with the latest archives having extended tool support. The Ensembl USEast and Asia mirrors of the current main site will be retired over the transition period this summer.

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by ·Comments Off on New visualisation of genomic variants in the context of genomic alignments 

We have developed a novel visualisation to enable the investigation of structural variants (SVs) in the context of functional elements, pairwise alignments and segmental duplications. Developed in collaboration with the Human Genomic Structural Variation Consortium (HGSVC), with genomic alignment data provided by the Human Pangenome Reference Consortium (HPRC), the new Alignments viewer makes it easier to explore haplotype-specific variation.

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