10 May, 2008

Coming back from CSHL

I'm in the airline lounge about to head back from "Biology of Genomes" at Cold Spring Harbor Laboratory. As always, it was a great meeting; highlights for me was seeing the 1,000 genomes data starting to flow - it is clear that the shift in technology is going to change the way we think about population genomics - and for me, the best session was one on "non-traditional models" - Dogs, Horses and Cows, where the ability to do cost effective genotyping has completely revolutionised this field. Now the peculiarities of the breeding structures, with Dog breeds being selected for diverse phenotypes, Cows with the elite bulls siring thousands of offspring due to artificial insemination and Horses having obsessive trait fixation over the last 1,000 years can really bring power to genetics in different ways. Expect alot more knowledge to come from these organisms and others (chickens, pigs, sheep...) over the coming years.

For my own group, Daniel Zerbino talked about Velvet, our new short read assembler which has also just been published in Genome Research (link). Velvet is now robust and capable of assembling "lower" eukaryotic genomes - certainly up to 300MB from short reads in read pair format. It is also being extensively used by other groups, often for partial, minature de novo assemblies in regions. It went down well, and Daniel handled some pretty tricky questions in the Q&A afterwards. Next up - we get access to a 1.5TB real memory machine, and put a whole human genome WGS into memory. Alison (Meynert) and Michael (Hoffman) had great posters on cis-regulation and looked completely exhausted at the end of their poster session.

From Ensembl, Javier talked about Enredo-Pecan-Ortheus (which we often nickname as EPO) pipeline. As some said afterwards to us "you've really solved the problem, haven't you" - Javier was able to show clear evidence that each component was working well, better than competitive methods, and having a impact on real biological problems, for example, derived allele frequency. Its ability to handle duplications is a key innovation. Javier and Kathryn are current wrestling in the "final" 2x genomes into this framework, from which point we will start to have a truly comprehensive grasp on mammalian DNA alignments. I also like it as Enredo is another "de bruijn graph" like mechanism. Currently the joke is that about 10 minutes into any conversation I say "well, the right way to solve this problem is to put the DNA sequence into a de bruijn graph".

Going to CSHL biology of genomes is always a little wince making though as this field - high end genomics - really prefers to use the UCSC Genome Browser (which as I've written before on, is a good browser, and I take the use of it to be our challenge to make better interfaces for these users on our side). My informal counting of screen shots was > 20 UCSC, 4 Ensembl (sneaking one case of 'Ensembl genes' shown in the UCSC browser as a point for each side) and 0 NCBI shots. Well. It just shows the task ahead of us. e50! - our user interface relaunch - is coming together, and we will start focus-group testing soon - time for us to address our failings head on. I'll be blogging more about this as we start to head towards broader testing.

Lots more to write about potentially - Neanderthals, Francis Collins singing in the NHGRI band (quite an experience), reduced representation libraries with Elliott, genome wide association studies (of which, I just _love_ the basic phenotype measures, from groups like Manolis Dermitzakis) and structural variation... but for the moment I've got to persuade my body to feel as if it is 11.30 at night and see if I can get a good nights sleep on the plane.


Max said...

New alignment-pipelines are always interesting. Is there any detailed documentation about your enredo-pecan-ortheus-pipeline on the internet (or about the current compara pipeline) or is the source code available from the ensembl cvs servers?

Ensembl Helpdesk (Giulietta) said...


Yes, this information is available. Leave us an email at:
and we will point you to the source code.