Difference between revisions of "SOAPdenovo"

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[[Category:Software]][[Category:Bioinformatics]]
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[[Category:Software]][[Category:Biology]][[Category:NGS]]
 
{|<!--Main settings - REQUIRED-->
 
{|<!--Main settings - REQUIRED-->
 
|{{#vardefine:app|soapdenovo}}
 
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SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.
 
SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.
  
==Installed Versions==
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31, 63 and 127 maximum kmer size versions are available as SOAPdenovo31mer (SOAPdenovo binary), SOAPdenovo-63mer, and SOAPdenovo-127mer binaries.
* 1.05 - 31, 63 and 127 kmer versions are available as SOAPdenovo31mer, SOAPdenovo63mer and SOAPdenovo127mer
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<!-- -->
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soapdenovo/2.04 module includes GapCloser.
==Required Modules==
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<!--Modules-->
[[Modules|modules documentation]]
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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}}
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_SOAPDENOVO_BIN - executable directory
 
* HPC_SOAPDENOVO_BIN - executable directory
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==

Latest revision as of 00:05, 22 August 2022

Description

soapdenovo website  

SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.

31, 63 and 127 maximum kmer size versions are available as SOAPdenovo31mer (SOAPdenovo binary), SOAPdenovo-63mer, and SOAPdenovo-127mer binaries.

soapdenovo/2.04 module includes GapCloser.

Environment Modules

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

System Variables

  • HPC_SOAPDENOVO_DIR - installation directory
  • HPC_SOAPDENOVO_BIN - executable directory