[ged] GED journal club tomorrow at 12pm.

[Jason Pell]

Hey Likit,

Can we postpone journal club due to SNOWPOCALYPSE 2011?  :D

Jason

On Tue, Feb 1, 2011 at 1:35 PM, Likit Preeyanon <preeyano at msu.edu> wrote:
> QP will be talking about Jellyfish.
>
> A fast, lock-free approach for efficient parallel counting of occurrences
> of k-mers
>
> Guillaume Marçais1,* and
> Carl Kingsford
>
>  Counting the number of occurrences of every k-mer (substring of length k)
> in a long string is a central subproblem in many applications, including
> genome assembly, error correction of sequencing reads, fast multiple
> sequence alignment, and repeat detection. Recently, the deep sequence
> coverage generated by next-generation sequencing technologies has caused the
> amount of sequence to be processed during a genome project to grow rapidly,
> and has rendered current k-mer counting tools too slow and memory intensive.
> At the same time, large multi-core computers have become commonplace in
> research facilities allowing for a new parallel computational paradigm.
> We propose a new k-mer counting algorithm and associated implementation,
> called Jellyfish, which is fast and memory efficient. It is based on a
> multi-threaded, lock-free hash table optimized for counting k-mers up to 31
> bases in length. Due to their flexibility, suffix arrays have been the data
> structure of choice for solving many string problems. For the task ofk-mer
> counting, important in many biological applications, Jellyfish offers a much
> faster and more memory efficient solution.
> http://bioinformatics.oxfordjournals.org/content/early/2011/01/07/bioinformatics.btr011.abstract
> See you.
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>