Difference between revisions of "SOAPdenovo"
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__NOTOC__ | __NOTOC__ | ||
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]] |
{|<!--Main settings - REQUIRED--> | {|<!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|soapdenovo}} | |{{#vardefine:app|soapdenovo}} | ||
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soapdenovo/2.04 module includes GapCloser. | soapdenovo/2.04 module includes GapCloser. | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * 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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WRITE CITATION HERE | WRITE CITATION HERE | ||
|}} | |}} | ||
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Latest revision as of 00:05, 22 August 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