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 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.

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by ·Comments Off on Ensembl launches COVID-19 resource

Today, Ensembl has joined the international scientific effort to tackle the COVID-19 pandemic. COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has spread rapidly since emerging in late 2019. Our SARS-CoV-2 genome browser and related resources at covid-19.ensembl.org are intended to support both basic research and ongoing work to develop treatments, diagnostics and vaccines.

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by ·Comments Off on Changes to FTP directory layout in Ensembl Genomes 43 / Ensembl 96

We will make changes to the directory layouts of both the Ensembl Genomes FTP server (ftp://ftp.ensemblgenomes.org/pub/) and the Ensembl GRCh37 FTP server (ftp://ftp.ensemblorg.ebi.ac.uk/pub/grch37/) that may affect your pipelines. These changes will come into effect in Ensembl Genomes release 43/Ensembl release 96, which are scheduled for April 2019. Here are the details, so that you can plan any required updates to existing scripts and pipelines ahead of the releases.
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