[ged] GED journal club tomorrow at 12pm.

[Likit Preeyanon]

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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