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 2.2.4. Freely available for every user 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-2.2.4
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