Jellyfish: Difference between revisions

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[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
[[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==
==Environment Modules==
===Serial===
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 - installation directory
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
* HPC_{{#uppercase:{{#var:app}}}}_BIN - includes directory
* HPC_{{uc:{{#var:app}}}}_BIN - includes directory
<!--Configuration-->
<!--Configuration-->
{{#if: {{#var: conf}}|==Configuration==
{{#if: {{#var: conf}}|==Configuration==
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__NOTOC____NOEDITSECTION__
__NOTOC____NOEDITSECTION__
=Validation=
* Validated 4/5/2018

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