Difference between revisions of "Jellyfish"
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{#uppercase:{{#var:app}}}}_DIR | + | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory |
| + | * HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_BIN - includes directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 00:09, 3 April 2014
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