Jellyfish (DISABLED - Will be removed on 1/24/2018)

Note: Due to lack of use, this software module has been disabled and will be removed from MSI systems on 1/24/18. If you need this software, please contact help@msi.umn.edu.

 

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 using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.

Website: http://www.cbcb.umd.edu/software/jellyfish/

To run this software interactively in a Linux environment run the commands:

module load jellyfish
jellyfish
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