Difference between revisions of "ALLPATHS-LG"
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Moskalenko (talk | contribs) (Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:Bioinformatics <!-- ######## Template Configuration ######## --> <!--Edit definitions of the variables used in temp...") |
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<!--Main settings - REQUIRED--> | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|allpathslg}} | |{{#vardefine:app|allpathslg}} | ||
|{{#vardefine:url|http://www.broadinstitute.org/software/allpaths-lg/blog/}} | |{{#vardefine:url|http://www.broadinstitute.org/software/allpaths-lg/blog/}} | ||
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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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{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
| − | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | + | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} |
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ALLPATHS-LG is a short read assembler. It has been designed to use reads | ALLPATHS-LG is a short read assembler. It has been designed to use reads | ||
produced by new sequencing technology machines such as the Illumina Genome | produced by new sequencing technology machines such as the Illumina Genome | ||
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to, reads of length 100 bases. ALLPATHS is not designed to assemble Sanger | to, reads of length 100 bases. ALLPATHS is not designed to assemble Sanger | ||
or 454 FLX reads, or a mix of these with short reads. | or 454 FLX reads, or a mix of these with short reads. | ||
| − | <!-- | + | <!--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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| − | < | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
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| − | {{ | + | {{#if: {{#var: exe}}|==Additional Information== |
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WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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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== | ||
Latest revision as of 12:36, 12 August 2022
Description
ALLPATHS-LG is a short read assembler. It has been designed to use reads produced by new sequencing technology machines such as the Illumina Genome Analyzer. This version has been optimized for, but not necessarily limited to, reads of length 100 bases. ALLPATHS is not designed to assemble Sanger or 454 FLX reads, or a mix of these with short reads.
Environment Modules
Run module spider allpathslg to find out what environment modules are available for this application.
System Variables
- HPC_ALLPATHSLG_DIR - installation directory