If you are filtering a set of variants to look for those potentially involved in disease, your first stop will probably be databases of phenotype associations, like ClinVar. There is also a lot of valuable information on variant-disease associations in the literature, which may not yet have been extracted into curated databases. It can be hard to compile lists of citations for a large set of variants, but Ensembl VEP is here to help!Continue reading
Author: Astrid (Outreach)
The Ensembl VEP does not only allow you to annotate short variants, such as SNPs and short insertions or deletions, but also some types of structural variants.
Can you believe it? Our next release will be Ensembl 100! We are planning to release it along with Ensembl Genomes 47 at the end of April 2020. As with all releases, please note that these are intentions and are not guaranteed to make it into the releases.Continue reading
Google Summer of Code (GSoC) is a programme that has been set up by Google to introduce students to open source software development. It links students to open source organisations such as Ensembl. The students work remotely with their GSoC project mentors during the university summer break and get paid for it by Google. Both students and organisations go through a rigorous application and selection process. It ensures that the students are among the very best and that the organisations are committed to mentoring them and their projects effectively. We think that GSoC is a great programme for students as well as Ensembl as an open source organisation and are glad that we had the opportunity to be part of it again this year!
These releases are huge in many respects, so it was difficult to decide which news to put first! Let’s start with some exciting news from our annotators.Continue reading
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.
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!