The Genome Reference Consortium (GRC) plans to release a new human assembly (GRCh38) later this year. What is the reason for an update? The current human genome in Ensembl, UCSC and NCBI (GRCh37) is indeed high quality. The GRC reports it’s accurate to an error rate of ~1 in 100,000 bases. However, there are still gaps in the assembly and there are a number of difficult loci still to be resolved. The new update addresses many of these issues. More reasons for the update can be found on the GRC blog.
The new assembly will be available in Ensembl next year (the third or fourth quarter of 2014). What happens between the public release of the updated human assembly and the Ensembl release of the annotated genome? A series of posts from our team will cover the work required to annotate genes, variants, and more to a high standard. These articles will reflect not only the efforts to deliver high quality annotation, but to integrate the data in a useful way for our users. At least one post each month will reflect our thorough analysis of the genome in the following areas:
- Release cycle (how does it work?)
- The GRCh38 assembly
- The new regulation build– integration of ENCODE and Blueprint data
- Coordinate mapping from one assembly version to another
- Processing dbSNP and other sources of variants
- High quality genes, annotating the GENCODE set
- Updates to the Variant Effect Predictor (VEP)
- Determining stable ids for the new gene set
- Whole Genome Alignments– pairing up the new human assembly with other species
- Quality control- how do we check our data?
Keep your eye on our blog for more posts in this series, marked with the category “GRCh38 Ensembl”.
We’d like to announce our new, filmed browser workshop.
Take it for free on EBI’s Train Online platform!
You can either go through the whole day course top to bottom, or pick your favourite module. It’s complete with filmed presentations, exercises and answers, and links to more information.
Ensembl (many thanks to Emily Pritchard for putting this together) worked with EBI’s Outreach and Training team’s Mark Adams (who filmed the workshop and did all the slide and video processing).
We’re hosting a live webchat to take questions about any aspect of the course, so join us there on either date:
- Wed 3 April 4-5pm (GMT+1)
- Wed 17 April 4-5pm
Like the course? You might want to fly one of us out there to teach at your institute!
Questions/comments are very welcome at our helpdesk.
The Wellcome Trust Genome Campus as well as the Sanger Institute and the EBI are closed for the holiday period between 23 December and 2 January. Ensembl browsers (www.ensembl.org, useast.ensembl.org. uswest.ensembl.org. and asia.ensembl.org) along with underlying databases will remain accessible during this time, however, if we experience any issues, associated fixes are likely to be delayed.
As usual, API or local installation issues can be reported to our developer mailing list (the archive is searchable at http://lists.ensembl.org/pipermail/dev/), and questions or reports about the browser or underlying data can be emailed to helpdesk (this is a private list). However, please expect delays in replying to your question up to 4 January 2013.
Have a good end to the year. We look forward to hearing from you in 2013.
To all wet-labbers, Ensembl browser beginners and intermediates,
Did you ever wish that an expert in the Ensembl browser would take you through the views, and explain what we have to offer? (And how to get it?)
Now’s your chance! If you’re in California, and could host a browser workshop, just email me (firstname.lastname@example.org) about it. Details of our workshops are here.
We’re hoping to come out there around the ASHG, and offer workshops before the 6 and/or after the 10 November.
Ensembl is in Uruguay! We’re teaching a workshop alongside instructors from VEGA/HAVANA, Janelia Farm Research Campus, Duke University Center for Human Genetics, and University of Maryland. The Open Door Workshop is funded by the Wellcome Trust, and provides different bioinformatics tools to analyse the human genome. At our workshop this week, we have professors and researchers from nine different countries in South and Central America.
Our training manual is on the Open Door Workshop page, so go ahead and check it out if you want to know more. And remember, if you would like to host an Ensembl browser workshop at your institute, contact us!
If you’re at the Biocuration conference currently happening in Washington DC, feel free to swing by the poster of Amonida Zadissa to learn about the Ensembl gene set (poster number P.87).
Ensembl Genebuild members will also be attending:
5th International Conference on Primate Genomics Bronwen Aken
17-19 April 2012
Houston, Texas, USA
Recomb 2012 Thibaut Hourlier, Poster 276
First session, 21st April, 18:30-20:00
Conference on Research in Computational Molecular Biology
21-24 April 2012
Ensembl archive sites allow you to browse older versions of our website (and the underlying data). These are maintained going back three years from the live version.
Versions 50-52 of the website (2008) will be retired tomorrow (30 March). Data and code for these releases are still available using MySQL or the Perl API. No major genome assembly changes are included in these versions.
Archives are especially useful in citing our webpages in publications. As Ensembl has frequent updates (every two months) it is useful to use the ‘permalink’ found at the bottom left of Ensembl views.
The url will follow the format of this example:
and will bring the reader to that specific Ensembl version, rather than the live site (at www.ensembl.org).
The Ensembl Team
I am working in Ensembl Outreach, and I’d like to point you to some new videos we have on our YouTube channel. These 5 videos were requested from clinical researchers at the Erasmus MC in Rotterdam.
The Ensembl Overview takes you through some Ensembl data and analysis, with a focus on where the gene set comes from, and sequence variations.
Four short clips between two and five minutes each show you:
We’d like to know what other videos you want to watch. Drop me an email, or add as a comment to this post. Thanks!
Giulietta (Ensembl Outreach)
Due to a network problem, all of the Ensembl Genomes sites such as http://plants.ensembl.org and http://www.ensemblgenomes.org are currently offline. Other EBI services are also affected (including ENA and EGA). Our network providers are working to fix the problem, and will have EBI resources back online when possible.
The Ensembl website is live and unaffected. Biomart provides access to Ensembl Genomes data during this period.
[UPDATE: All services are operating normally.]
The Ensembl and Ensembl Genomes teams
The Ensembl Genomes Project is pleased to announce release 12 of Ensembl Genomes.
This release contains 5 new genomes, bringing the total genomes supported to 335. Main highlights are:
* Software migration to Ensembl 65
* Operon data from RegulonDB for E. coli K12 in Ensembl Bacteria
* A new species (Ashbya gossypii) and manually curated annotation from a new resource for yeast! This is the first release of Ensembl Fungi containing data from PomBase, a new genome-centric resource (developed by Ensembl Genomes, the University of Cambridge, and University College London) for the fission yeast Schizosaccharomyces pombe.
* The addition of Cyanidioschyzon merolae to Ensembl Plants and significant updates to Physcomitrella patens and the soybean Glycine max
* Three new genomes in Ensembl Metazoa: Atta cephalotes, a leaf-cutting ant, Tribolium castaneum, the red flour beetle, and Bombyx mori, a domesticated silkmoth
Note, EG 12 will be available on ftp next week.
The Ensembl Genomes Team