[ged] Paper for journal club 1/31

[Jason Pell]

Hi everyone,

Just sending out a quick reminder about tomorrow. Journal club is at
11am tomorrow in room 2228. Hope to see you there.

Jason

On Thu, Jan 26, 2012 at 12:18 PM, Timothy Brom <bromtimo at cse.msu.edu> wrote:
> I am going to be (at least attempting to) present the following paper at
> the journal club meeting on 1/31
>
> http://genome.cshlp.org/content/early/2011/12/07/gr.126953.111.abstract
>
> Efficient de novo assembly of large genomes using compressed data
> structures
> Jared T Simpson and Richard Durbin
>
> Abstract
> De novo genome sequence assembly is important both to generate new
> sequence assemblies for previously uncharacterized genomes and to
> identify the genome sequence of individuals in a reference-unbiased
> way. We present memory efficient data structures and algorithms for
> assembly using the FM-index derived from the compressed
> Burrows-Wheeler transform, and a new assembler based on these called
> SGA (String Graph Assembler). We describe algorithms to error correct,
> assemble and scaffold large sets of sequence data. SGA uses the
> overlap-based string graph model of assembly, unlike most de novo
> assemblers that rely on de Bruijn graphs, and is simply
> parallelizable. We demonstrate the error correction and assembly
> performance of SGA on 1.2 billion sequence reads from a human genome,
> which we are able to assemble using 54 GB of memory. The resulting
> contigs are highly accurate and contiguous, while covering 95% of the
> reference genome (excluding contigs less than 200bp in length).
> Because of the low memory requirements and parallelization without
> requiring inter-process communication, SGA provides the first
> practical assembler to our knowledge for a mammalian-sized genome on a
> low-end computing cluster.
>
> Jason - Thanks for the suggestion.
>
> --
> Tim Brom
> bromtimo at cse.msu.edu
>
>
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