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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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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This blog post is a joint contribution by Joannella Morales, Jane Loveland, Adam Frankish, Fiona Cunningham and Astrid Gall.

We are pleased to introduce the Matched Annotation from the NCBI and EMBL-EBI (MANE) project. This new joint initiative between EMBL-EBI’s Ensembl project and NCBI’s RefSeq project aims to release a genome-wide transcript set that contains one well-supported transcript per protein-coding locus. All transcripts in the MANE set will perfectly align to GRCh38 and will represent 100% identity (5’UTR, coding sequence, 3’UTR) between the RefSeq (NM) and corresponding Ensembl (ENST) transcript.
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This guest blog is a joint contribution by Laura Harris (GWAS Catalog) and Astrid Gall (Ensembl Outreach). You can contact our colleagues of the GWAS Catalog at gwas-info[at]ebi.ac.uk.

This year marks a special anniversary for the GWAS Catalog, as we have reached ten years since our launch in 2008. The GWAS Catalog is a widely used publicly available resource of all published human genome wide association studies (GWAS) and association results. Each GWAS study contains a wealth of information which is effectively inaccessible to researchers and clinicians without them spending a lot of time undertaking regular systematic reviews of the literature. This is where we can help you!

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