The layout of the Ensembl Raid Release FTP site will be updated in Rapid Release version 40, due in November 2022.

In order to present the ever-increasing data in Ensembl Rapid Release more clearly, we are updating the layout of the FTP site to present separate annotation sets for the same genome assembly. A new subdirectory containing all annotation, assembly and statistic files will be added to indicate the annotation source.

For example, the following FTP file path for the Asterias rubens gene annotation will change from:

http://ftp.ensembl.org/pub/rapid-release/species/Asterias_rubens/GCA_902459465.3/geneset/

to:

http://ftp.ensembl.org/pub/rapid-release/species/Asterias_rubens/GCA_902459465.3/ensembl/geneset/

and

http://ftp.ensembl.org/pub/rapid-release/species/Asterias_rubens/GCA_902459465.3/refseq/geneset/

to reflect the two available genesets from different annotation sources.

This change will affect all species, so even species with a single annotation source will have the appropriate ‘source’ subdirectory added to the FTP file path.

These changes may affect existing configurations for automatically downloading files from the Ensembl Rapid Release FTP site. If you have any questions about the planned changes, please contact us on the Ensembl Helpdesk.