Difference between revisions of "SOAPdenovo"
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[[Category:Software]][[Category:Bioinformatics]] | [[Category:Software]][[Category:Bioinformatics]] | ||
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|{{#vardefine:app|soapdenovo}} | |{{#vardefine:app|soapdenovo}} | ||
|{{#vardefine:url|http://soap.genomics.org.cn/soapdenovo.html}} | |{{#vardefine:url|http://soap.genomics.org.cn/soapdenovo.html}} | ||
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|{{#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. | ||
| − | + | 31, 63 and 127 maximum kmer size versions are available as SOAPdenovo31mer (SOAPdenovo binary), SOAPdenovo-63mer, and SOAPdenovo-127mer binaries. | |
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| − | <!-- --> | + | soapdenovo/2.04 module includes GapCloser. |
| − | + | <!--Modules--> | |
| − | + | ==Environment Modules== | |
| + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
| + | ==System Variables== | ||
| + | * 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 | + | {{#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== | ||
Revision as of 17:23, 10 June 2022
Description
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