Difference between revisions of "ALLPATHS-LG"

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(Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:Bioinformatics <!-- ######## Template Configuration ######## --> <!--Edit definitions of the variables used in temp...")
 
 
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__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
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[[Category:Software]][[Category:Bioinformatics]]
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[[Category:Software]][[Category:Biology]][[Category:NGS]]
<!-- ########  Template Configuration ######## -->
 
<!--Edit definitions of the variables used in template calls
 
Required variables:
 
app - lowercase name of the application e.g. "amber"
 
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
Optional variables:
 
INTEL - Version of the Intel Compiler e.g. "11.1"
 
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
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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/}}
<!--Compiler and MPI settings - OPTIONAL -->
 
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
 
<!--Choose sections to enable - OPTIONAL-->
 
<!--Choose sections to enable - OPTIONAL-->
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
|{{#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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<!--Description-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
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{{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.
<!--Location-->
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<!--Modules-->
{{App_Location|app={{#var:app}}|{{#var:ver}}}}
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==Environment Modules==
==Available versions==
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* 39099 (Nov 2011)
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==System Variables==
<!-- -->
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
{{#if: {{#var: mod}}|==Running the application using modules==
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<!--Additional-->
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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{{#if: {{#var: exe}}|==Additional Information==
* HPC_ALLPATHSLG_BIN - executable directory
 
* HPC_ALLPATHSLG_DOC - documentation directory
 
{{#if: {{#var: exe}}|==How To Run==
 
 
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 policy==
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{{#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

allpathslg website  

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