A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.

ABSTRACT:

Motivation

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 multicore computers have become commonplace in research facilities allowing for a new parallel computational paradigm.

Results

We propose a new k-mer counting algorithm and associated implementation, called Jellyfish, which is fast and

SUBMITTER: Marcais G 

PROVIDER: S-EPMC3051319 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature