JellyFish

Overview

Jellyfish 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.

Version 2.2.7 is installed on the iCSF.

Restrictions on use

The software is free to use, Jellyfish is distributed as source code under the GPL license Please see the GPL License page for more details.

Set up procedure

To access the software you must first load the modulefile:

module load apps/gcc/jellyfish/2.2.7

Running the application

jellyfish <cmd> [options] arg...
Where <cmd> is one of: count, bc, info, stats, histo, dump, merge, query, cite, mem, jf.
Options:
  --version        Display version
  --help           Display this message

Further info

• Jellyfish website

Updates

None.