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.
Author: Ben (Outreach)
This month we’re meeting Paul Kersey, who is the Ensembl Genomes team leader.
This month we’re meeting Dan Staines, who is part of the Ensembl Production team.
We’re really excited to be a part of the ASHG conference again, this time in Orlando from the 17th-21st October. We can’t wait to see all the great science that’s going to be presented, but here’s a guide to the talks, workshops and posters from Ensembl and some of our close friends:
Ensembl 91 is scheduled for December 2017 and we’re continuing our push to include the genome annotation for lots of new species. This time, we’re adding a whole new set of primate species to Ensembl.
Here’s what you can look forward to:
New assemblies, gene sets and annotations
- Annotation of 12 new primate genomes, as well as updates to 6 existing genomes:
- Nancy Ma’s night monkey
- White-headed capuchin
- Sooty mangabey
- Angola colobus
- Crab eating macaque
- Southern pig-tailed macaque
- Coquerel’s sifaka
- Black snub-nosed monkey
- Golden snub-nosed monkey
- Black-capped squirrel monkey
- Chimpanzee (update)
- Gibbon (update)
- Gorilla (update)
- Mouse lemur (update)
- Olive baboon (update)
- Tarsier (update)
- Annotation on the latest Cat genome assembly, Felis_catus_8.0
- C. elegans gene set and annotation updated to Wormbase release WS260
- Fruitfly gene set and annotation updated to Flybase release FB2017_04 (dmel_r6.17)
- Updated Human cDNA alignments
- Updated Mouse cDNA alignments
- Updated microarray probe mappings and comparative genomics analyses for all new and updated species
Other updates and highlights
- Updating our human variation database with:
- COSMIC 82 somatic variants
- HGMD 2017.2
- DGVa structural variants
- Phenotypes from NHGRI-EBI GWAS, OMIM, ClinVar, UniProt, Cosmic Gene Census, DDG2P, MIM Morbid and Orphanet
- In other species we also have variation updates as follows:
- dbSNP 150 in macaque, mouse, zebrafish, sheep, pig, horse, cow and chicken
- DGVa in cow, dog and mouse, horse, macaque, pig, sheep and zebrafish
- Phenotype updates from relevant databases in rat, zebrafish and mouse
- Links to PharmGKB added from human variants
- New web tool for Linkage Disequilibrium (LD) calculation
- Updated GRCh37 regulatory features
For more details on the declared intentions, please visit our Ensembl admin site. Please note that these are intentions and are not guaranteed to make it into the release.
In the latest Ensembl release (Ensembl 90, August 2017), we have added the option for you to adjust the y-axis of your custom “wiggle” tracks, such as BigWig and bedGraph files.
We are pleased to announce that Ensembl Genomes 36 has now been released, which includes new and updated genome assemblies and gene annotation as well as updated variation data and comparative genomics analyses. Find out more below:
- Ensembl Bacteria includes an additional 142 genomes from release 35 together with an update to gene families.
- Ensembl Fungi has added gene symbols for 1-to-1 orthologues from S. cerevisiae to Botrytis cinerea and includes updated PHI-base 4.3 annotations.
- Ensembl Metazoa now has automated RNA gene annotation for 37 species (i.e. all species that have not been imported from FlyBase, VectorBase or WormBase) and alignment of Rfam 12.2 covariance models for all species. There are also updated protein features, which now includes features from new sources (CDD, MobiDB and SFLD).
- Ensembl Protists now has new automatic ncRNA alignments across all protist species as well as updated PHI-base 4.3 annotations.
- Ensembl Plants now includes the new genome assembly for Hordeum vulgare (barley), the biggest diploid yet sequenced, which is included in updated comparative peptide analyses for all species. There are also new ncRNA gene annotations and new plant reactome cross references across all plant species. New and updated variation data has also been included in this release for both Oryza sativa and Arabidopsis thaliana. Last, but not least, 80829 variation markers from the iSelect 90k array and 13.8 million Inter-Homoeologous Variants (IHVs) have been added to the wheat assembly, along with chloroplast and mitochondrial components (including gene annotations) imported from ENA.
Please see the release notes for full details of the updates.
Ensembl 89 is now live. Read on to find out about the new features and data in this release.Continue reading