A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.
Identifieur interne : 002486 ( Main/Exploration ); précédent : 002485; suivant : 002487A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.
Auteurs : Guillaume Marçais [États-Unis] ; Carl KingsfordSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2011.
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- MESH :
English descriptors
- KwdEn :
- MESH :
Abstract
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.
DOI: 10.1093/bioinformatics/btr011
PubMed: 21217122
Affiliations:
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Le document en format XML
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<front><div type="abstract" xml:lang="en">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.</div>
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