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Jellyfish

May 26, 2018

Fast, memory-efficient counting of k-mers in DNA

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 quickly by using an efficient encoding of a hash table and by exploiting the “compare-and-swap” CPU instruction to increase parallelism.

WWW http//www.genome.umd.edu/jellyfish.html