[ged] Fwd: Paper for Wednesday GED journal club

[Likit Preeyanon]

Hi,

Meet at the same room at the noon. :)

Jason is talking about the new version of ALLPATHS assembler. Find the paper below.

Begin forwarded message:

> From: Jason Pell <jason.pell at gmail.com>
> Date: February 25, 2011 10:53:14 PM EST
> To: ged-jclub at lists.idyll.org
> Subject: [ged] Paper for Wednesday
> 
> Hi everyone,
> 
> On Wednesday, I will present the paper entitled "High-quality draft
> assemblies of mammalian genomes from massively parallel sequence
> data." This is the latest version of the ALLPATHS assembler, which is
> designed to assemble mammalian-sized genomes. I will probably just
> focus more on the evolution of ALLPATHS (to show how it works compared
> to other assemblers) and then discuss some of the improvements they
> have made to it in the most recent version.
> 
> http://www.pnas.org/content/early/2010/12/20/1017351108.abstract
> 
> Here is the abstract:
> 
> Massively parallel DNA sequencing technologies are revolutionizing
> genomics by making it possible to generate billions of relatively
> short (∼100-base) sequence reads at very low cost. Whereas such data
> can be readily used for a wide range of biomedical applications, it
> has proven difficult to use them to generate high-quality de novo
> genome assemblies of large, repeat-rich vertebrate genomes. To date,
> the genome assemblies generated from such data have fallen far short
> of those obtained with the older (but much more expensive)
> capillary-based sequencing approach. Here, we report the development
> of an algorithm for genome assembly, ALLPATHS-LG, and its application
> to massively parallel DNA sequence data from the human and mouse
> genomes, generated on the Illumina platform. The resulting draft
> genome assemblies have good accuracy, short-range contiguity,
> long-range connectivity, and coverage of the genome. In particular,
> the base accuracy is high (≥99.95%) and the scaffold sizes (N50 size =
> 11.5 Mb for human and 7.2 Mb for mouse) approach those obtained with
> capillary-based sequencing. The combination of improved sequencing
> technology and improved computational methods should now make it
> possible to increase dramatically the de novo sequencing of large
> genomes. The ALLPATHS-LG program is available at
> http://www.broadinstitute.org/science/programs/genome-biology/crd.
> 
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