Both Ensembl release 97 and Ensembl Genomes release 44 are scheduled for mid- to late-June.

Included are a number of new livestock, fish, metazoan, plant, and protist genomes and genebuilds, as well as updates to the mouse and human GENCODE annotation and the human regulatory build.

Read on to see further details of the new data you can look forward to.

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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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In the next release of Ensembl (Ensembl 96) we will remove our ontology database patching scripts from the main Ensembl repository.

There is now a dedicated module using the EBI OLS service to load Ensembl required ontologies. Considering this module is now in charge of loading the required data, the previous databases patches have been moved to the ols-ensembl-loader repository.

If you need to update your system with future patches, please now refer to the ols-ensembl-loader repository sql directory where files are already available.

Please contact the Ensembl Helpdesk if you have any questions or want to find out more about how this might affect your work.

We are planning to release Ensembl 96 and Ensembl Genomes 43 in late March or beginning of April 2019.

The Ensembl 96 release includes the first pass full annotation of the mouse genome, with the GENCODE M21 gene set.

The Ensembl Genomes 43 release will bring changes to our REST API and FTP server that may affect your pipelines. Specifically, we will merge our Ensembl and Ensembl Genomes REST servers into a single server. We will also change the Ensembl Genomes Comparative Genomics FTP file structure to make it consistent with Ensembl.

We have got lots of new genomes: 19 birds, five reptiles and 12 mammals, which include primates, rodents, American mink, American bison and wild yak.

We also have an exciting first release of Ensembl-RefSeq MANE Select v0.5 transcripts!

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