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.
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.
Version 2.1.3. Freely available for every user. Version 1.1.11. This version works with Quake.
Initialize module with command:
module add jellyfish-2.1.3 module add jellyfish-1.1.11
Documentation is available in JellyfishUserGuide.pdf or it's local copy at /software/jellyfish-2.1.3/share/doc/JellyfishUserGuide.pdf.