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 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 Expanded 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.

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