JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the “compare-and-swap” CPU instruction to increase parallelism.
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Bioinformatics. 2011 Mar 15;27(6):764-70. doi: 10.1093/bioinformatics/btr011. Epub 2011 Jan 7.
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.
Marçais G, Kingsford C.