Difference between revisions of "Wgs"

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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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__NOTOC__
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[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
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{|<!--Main settings - REQUIRED-->
[[Category:Software]]
 
<!-- ########  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"
 
-->
 
{|
 
<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|wgs}}
 
|{{#vardefine:app|wgs}}
 
|{{#vardefine:url|http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Paget}}
 
|{{#vardefine:url|http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Paget}}
<!--Compiler and MPI settings - OPTIONAL -->
 
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
<!--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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|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 
|{{#vardefine:faq|}} <!--Enable FAQ section -->
 
|{{#vardefine:faq|}} <!--Enable FAQ section -->
|{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
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|{{#vardefine:citation|1}} <!--Enable Reference/Citation section -->
 
|}
 
|}
 
<!-- ########  Template Body ######## -->
 
<!-- ########  Template Body ######## -->
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Celera Assembler is scientific software for biological research. Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing. Celera Assembler has enabled many advances in genomics, including the first whole genome shotgun sequence of a multi-cellular organism (Myers 2000) and the first diploid sequence of an individual human (Levy 2007). Celera Assembler was developed at Celera Genomics starting in 1999. It was released to SourceForge in 2004 as the wgs-assembler under the GNU General Public License. The pipeline revised for 454 data was named CABOG (Miller 2008).
 
Celera Assembler is scientific software for biological research. Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing. Celera Assembler has enabled many advances in genomics, including the first whole genome shotgun sequence of a multi-cellular organism (Myers 2000) and the first diploid sequence of an individual human (Levy 2007). Celera Assembler was developed at Celera Genomics starting in 1999. It was released to SourceForge in 2004 as the wgs-assembler under the GNU General Public License. The pipeline revised for 454 data was named CABOG (Miller 2008).
<!--Location-->
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<!--Modules-->
{{App_Location|app={{#var:app}}|{{#var:ver}}}}
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==Required Modules==
== Available versions==
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[[Modules|modules documentation]]
* 6.1 release
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===Serial===
* 6.1-20110830 CVS - Developmental snapshot
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*{{#var:app}}
* 6.1-20120110 CVS - Developmental snapshot
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==System Variables==
* 6.1-20120117 CVS - Developmental snapshot
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* 7.0.1.22 (default)
 
<!-- -->
 
{{#if: {{#var: mod}}|==Running the application using modules==
 
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 
 
* HPC_WGS_BIN - executable directory
 
* HPC_WGS_BIN - executable directory
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
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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==
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*'''Q:''' **'''A:'''|}}
 
*'''Q:''' **'''A:'''|}}
 
{{#if: {{#var: citation}}|==Citation==
 
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{{app}}} you have to cite it as follows:
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If you publish research that uses {{#var:app}} you have to cite it as follows:
WRITE CITATION HERE
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 +
 
 +
Myers et al. (2000) [http://www.sciencemag.org/cgi/content/abstract/287/5461/2196 A Whole-Genome Assembly of Drosophila]. Science 287 2196-2204.
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 +
See the list of all related [http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page publications].
 
|}}
 
|}}
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__NOTOC____NOEDITSECTION__
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=Validation=
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* Validated 4/5/2018

Latest revision as of 21:29, 6 December 2019

Description

wgs website  

Celera Assembler is scientific software for biological research. Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing. Celera Assembler has enabled many advances in genomics, including the first whole genome shotgun sequence of a multi-cellular organism (Myers 2000) and the first diploid sequence of an individual human (Levy 2007). Celera Assembler was developed at Celera Genomics starting in 1999. It was released to SourceForge in 2004 as the wgs-assembler under the GNU General Public License. The pipeline revised for 454 data was named CABOG (Miller 2008).

Required Modules

modules documentation

Serial

  • wgs

System Variables

  • HPC_WGS_DIR - installation directory
  • HPC_WGS_BIN - executable directory




Citation

If you publish research that uses wgs you have to cite it as follows:


Myers et al. (2000) A Whole-Genome Assembly of Drosophila. Science 287 2196-2204.

See the list of all related publications.

Validation

  • Validated 4/5/2018