Jellyfish
Jump to navigation
Jump to search
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 - installation directory
- HPC_{{#uppercase:jellyfish}}_BIN - executable directory
- HPC_{{#uppercase:jellyfish}}_BIN - includes directory
Validation
- Validated 4/5/2018