Difference between revisions of "SOAPdenovo"

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m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==")
 
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__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
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[[Category:Software]][[Category:Bioinformatics]]
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[[Category:Software]][[Category:Biology]][[Category:NGS]]
<!-- ########  Template Configuration ######## -->
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{|<!--Main settings - REQUIRED-->
<!--Edit definitions of the variables used in template calls
 
Required variables:
 
app - lowercase name of the application e.g. "amber"
 
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
Optional variables:
 
INTEL - Version of the Intel Compiler e.g. "11.1"
 
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
-->
 
{|
 
<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|soapdenovo}}
 
|{{#vardefine:app|soapdenovo}}
 
|{{#vardefine:url|http://soap.genomics.org.cn/soapdenovo.html}}
 
|{{#vardefine:url|http://soap.genomics.org.cn/soapdenovo.html}}
<!--Compiler and MPI settings - OPTIONAL -->
 
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
<!--Choose sections to enable - OPTIONAL-->
 
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
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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.
{{#if: {{#var: mod}}|==Execution Environment and Modules==
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<!--Modules-->
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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==Environment Modules==
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
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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==
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{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
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{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==

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