Difference between revisions of "ALLPATHS-LG"
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Moskalenko (talk | contribs) m (Text replace - "{{#if: {{#var: mod}}|==Execution Environment and Modules== {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}" to "==Required Modules== modules documentation ===Serial=== *{{#var:app}}") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]] |
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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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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--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | == | + | ==System Variables== |
| − | *{{#var:app}} | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | + | <!--Additional--> | |
| − | + | {{#if: {{#var: exe}}|==Additional Information== | |
| − | {{#if: {{#var: exe}}|== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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