EMBL-EBI User Survey 2024

Do data resources managed by EMBL-EBI and our collaborators make a difference to your work?

Please take 10 minutes to fill in our annual user survey, and help us make the case for why sustaining open data resources is critical for life sciences research.

Survey link: https://www.surveymonkey.com/r/HJKYKTT?channel=[webpage]

FTP Download

You can download via a browser from our FTP site, use a script, or even use rsync from the command line.


For rapid bulk download of files, the Ensembl FTP site is available as an end point in the Globus Online system. In order to access the data you need to sign up for an account with Globus, install the Globus Connect Personal software and setup a personal endpoint to download the data. The Ensembl data is hosted at the EMBL-EBI end point called "EMBL-EBI Public Data". Data from the Ensembl FTP site can then be found under the "/ensemblorg/pub". You can also click here to open the target directory.

Species DNA (FASTA) cDNA (FASTA) Protein sequence (FASTA) Annotated sequence (EMBL) Whole databases GTF Variation (VEP) TSV

Pantaxonomic compara multi-species

Pantaxonomic compara multi-species data on the genomes provided by Ensembl Genomes is available from the FTP site in the following formats.

Ensembl Genomes: MySQL | TSV |