Jellyfish
Revision as of 00:09, 3 April 2014 by Moskalenko (talk | contribs)
Description
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.
Required Modules
Serial
- jellyfish
or
- gcc/4.7.2 jellyfish
System Variables
- HPC_{{#uppercase:jellyfish}}_DIR