Difference between revisions of "Jellyfish"

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(Created page with "Category:Software {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|jellyfish}} |{{#vardefine:url|http://www.genome.umd.edu/jellyfish.html}} <!--CONFIGURATION: OPTIONAL (...")
 
 
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[[Category:Software]]
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[[Category:Software]][[Category:Biology]][[Category:NGS]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|jellyfish}}
 
|{{#vardefine:app|jellyfish}}
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"jellyfish dump" command.
 
"jellyfish dump" command.
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
===Serial===
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
or
 
* gcc/4.7.2 {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 +
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
 +
* HPC_{{uc:{{#var:app}}}}_BIN - includes directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 19:27, 12 August 2022

Description

jellyfish website  

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.

Environment Modules

Run module spider jellyfish to find out what environment modules are available for this application.

System Variables

  • HPC_JELLYFISH_DIR - installation directory
  • HPC_JELLYFISH_BIN - executable directory
  • HPC_JELLYFISH_BIN - includes directory