Difference between revisions of "Wgs"

Latest revision as of 20:55, 12 August 2022

Description

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).

Environment Modules

Run module spider wgs to find out what environment modules are available for this application.

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.

@@ Line 1: / Line 1: @@
-__NOTOC__
+[[Category:Software]][[Category:Biology]][[Category:NGS]]
-__NOEDITSECTION__
+{|<!--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: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:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
@@ Line 26: / Line 9: @@
 |{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 |{{#vardefine:faq|}} <!--Enable FAQ section -->
-|{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
+|{{#vardefine:citation|1}} <!--Enable Reference/Citation section -->
 |}
 <!-- ########  Template Body ######## -->
 <!--Description-->
 {{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 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-->
+<!--Modules-->
-{{App_Location|app={{#var:app}}|{{#var:ver}}}}
+==Environment Modules==
-Available versions:
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
+==System Variables==
-.1 release - Default version
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
+* HPC_WGS_BIN - executable directory
-.1-20110830 CVS - Developmental version
-<!-- -->
-{{#if: {{#var: mod}}|==Running the application using modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
-To load the updated version run
- module load wgs/6.1-20110830
-If the perl module is not loaded run
- module load perl wgs
-or
- module load perl wgs/6.1-20110830
 {{#if: {{#var: exe}}|==How To Run==
 WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
@@ Line 55: / Line 29: @@
 {{#if: {{#var: pbs}}|==PBS Script Examples==
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
-{{#if: {{#var: policy}}|==Usage policy==
+{{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 {{#if: {{#var: testing}}|==Performance==
@@ Line 62: / Line 36: @@
 *'''Q:''' **'''A:'''|}}
 {{#if: {{#var: citation}}|==Citation==
-If you publish research that uses {{{app}}} you have to cite it as follows:
+If you publish research that uses {{#var:app}} you have to cite it as follows:
-WRITE CITATION HERE
+Myers et al. (2000) [http://www.sciencemag.org/cgi/content/abstract/287/5461/2196 A Whole-Genome Assembly of Drosophila]. Science 287 2196-2204.
+See the list of all related [http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page publications].
 |}}
+__NOTOC____NOEDITSECTION__