Updates to programmatic access to Ensembl and transitioning to the new Ensembl Platform

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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.

Timeline of key changes:

  • Spring 2026:
    • Current Ensembl APIs and public MySQL servers will receive their final update with the release of e!116
    • Ensembl FTP access points at ftp.ensembl.org and ftp.ensemblgenomes.ebi.ac.uk/pub will also receive their final update with the release of e!116
    • These resources will remain available for use but will no longer receive updates.
  • Summer 2026:
    • ensembl.org will redirect to the site currently hosted on beta.ensembl.org.
    • The Ensembl 116 (vertebrates) and Ensembl Genomes 63 (non-vertebrates) sites will move to our archive collection.
    • These archives will maintain enhanced tool functionality, including continued access to the Ensembl VEP web interface, for an extended period.
    • Enhanced tool functionality within archives will begin to be phased out once equivalent services are available on the new platform.
    • These archives will not have mirrors in US East and Asia

The new Ensembl data platform

As part of the transition, future datasets will be available only through the new platform at beta.ensembl.org. Programmatic access will shift to new and modernised services, including:

  • Ensembl GraphQL: a powerful and flexible way to query Ensembl data.
  • Ensembl refget: enables efficient sequence access using GA4GH-compliant identifiers.
  • Ensembl Beta FTP: provides bulk download access to updated data, though please note its structure is still evolving and will likely change.

What will stay the same?

  • Access to previous genome data will be possible through the Ensembl archives.
  • Archive sites will continue to support key tools such as the Ensembl Variant Effect Predictor (Ensembl VEP) for some time after the transition.
  • Most links pointing to ensembl.org will continue to work by redirecting to an appropriate page on the new site

What’s new?

All new genome data and tools will be delivered through the new platform at beta.ensembl.org. This site is being designed to make data easier to find and explore, and to improve how Ensembl grows in the future.

Features currently under development include:

  • A more intuitive design for browsing genomes.
  • Faster tools for finding genes, variants, and sequences.
  • New ways to download data as they become available.

What do you need to do?

For most Ensembl users who browse the website, you don’t need to take any immediate action. You can continue using the current Ensembl site as usual throughout early 2026. Once ensembl.org switches over, you will simply be redirected to the new site automatically.

If you use Ensembl for more advanced or programmatic access (e.g. APIs, custom pipelines), you may want to start planning for migration.

Stay connected

We’re very excited about this next chapter for Ensembl and look forward to sharing more updates over the coming months. We recommend subscribing to the Ensembl Dev mailing list to receive timely updates as they develop.

If you have questions, feedback or concerns, please get in touch with us via the Ensembl Helpdesk. Your input is incredibly valuable as we work to improve Ensembl for the whole community.