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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.

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.

Required Modules


  • jellyfish


  • gcc/4.7.2 jellyfish

System Variables

  • HPC_{{#uppercase:jellyfish}}_DIR - installation directory
  • HPC_{{#uppercase:jellyfish}}_BIN - executable directory
  • HPC_{{#uppercase:jellyfish}}_BIN - includes directory