The path to sequencing the wheat genome has been no easy ride, due to its large and highly repetitive genome. This new assembly from the IWGSC bridges many gaps from the initial genome sequencing effort. Read on to find out more about this exciting new genome assembly!
We’ve been tending the Ensembl Plants garden with great care, have cultivated several new species and updated a number of genome assemblies, including a new chromosome-level wheat genome from IWGSC. The protist team have also been busy and are proud to announce an updated assembly for Leishmania major.
Read on to find out more about these exciting new updates and more in this new release of Ensembl Genomes!
Are you feline excited for our new pawsome release?!
Ensembl 93 has been released, bringing with it two new big cat genomes for tiger and leopard, and an update to the domestic cat assembly. If cats aren’t your thing, we also have a huge new dbSNP import for human and a brand new regulatory build and GENCODE update for mouse.
We also have a new hagfish genome, important changes to our VEP REST endpoints, and many more exciting developments so read on to find out more!
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!
Functional genomics data from DANIO-CODE has been released to the public. This international effort, similar to ENCODE in human and mouse, seeks to characterise the functional elements in the zebrafish (Danio rerio) genome. Announced on Saturday at the International Zebrafish Conference, the DANIO-CODE dataset exists as a track hub, which can be viewed in Ensembl.
One of the biggest headaches when working with insertions and deletions is how many different ways you can represent the same variant. If you’re looking to find out if there’s already known allele frequencies or phenotypes at a locus, you want to make sure that you find the right one. The VEP can take that headache away through normalisation of variants.
For the third year in a row, we’re lucky to have student developers working with us as part of Google Summer of Code. We’ve got three GSOC-ers this year, working on some really exciting projects: Zeyu Tony Yang, working on primary genome analysis, Nabil Ibtehaz, working on transcript-level orthology and Somesh Chaturvedi, working on retrieving reference sequences with APIs.
GSOC is a project set up by Google that places students in open source projects to take on a short independent coding project, and pays them for it. We have to pass rigorous selection criteria to be allowed to offer projects on GSOC, and the students have to be selected by both Google and us to take part. It means the GSOC-ers are the Top Gun of student developers. We think this is a really great opportunity, both for open source projects like us, who get a fresh pair of eyes to take a look at something that we’ve maybe put on the back-burner, and for the students, who get experience working on a real-world coding project during their university summer break.
From Ensembl 93 onwards, we plan to recommend newer versions of Perl (5.14- 5.26) and BioPerl (1.6.924) when using the Ensembl Perl API. This may affect pipelines which employ the Ensembl Perl API, since we will no longer actively support older versions of Perl and BioPerl.
As of Ensembl release 93, which is due at the end of the month, the Gene Variant Image view will be retired for human. We have elected to retire this page because we feel that the density of known genetic variation is too great for this view to be informative in its current form.