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.

jellyfish is a command-line program that reads fasta and multi-fasta files containing dna sequences. it outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command.

this package contains the dynamic library the main executable of jellyfish is linked to.