[ged] GED journal club tomorrow at 12pm.

[C. Titus Brown]

Fine by me, but I expect you all to work online.  Proof of Internet
outage must be provided otherwise.

On Tue, Feb 01, 2011 at 04:45:26PM -0500, Jason Pell wrote:
> 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 Mar?ais1,*?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.
> > _______________________________________________
> > ged-jclub mailing list
> > ged-jclub at lists.idyll.org
> > http://lists.idyll.org/listinfo/ged-jclub
> >
> >
> 
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-- 
C. Titus Brown, ctb at msu.edu