Jellyfish

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Description

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.

Availability

Version 2.1.3. Freely available for every user. Version 1.1.11. This version works with Quake.

Licence

GPL 3

Use

Initialize module with command:

module add jellyfish-2.1.3
module add jellyfish-1.1.11

Documentation

Documentation is available in JellyfishUserGuide.pdf or it's local copy at /software/jellyfish-2.1.3/share/doc/JellyfishUserGuide.pdf.

Program manager

meta@cesnet.cz

Homepage

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