Difference between revisions of "ALLPATHS-LG"
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Moskalenko (talk | contribs) m (Text replace - "{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}" to "{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} ") |
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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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<!--Choose sections to enable - OPTIONAL--> | <!--Choose sections to enable - OPTIONAL--> | ||
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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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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--> |
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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