Revision as of 21:29, 6 December 2019

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).

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

@@ Line 1: / Line 1: @@
-__NOTOC__
+[[Category:Software]][[Category:Bioinformatics]][[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 ######## -->
@@ Line 34: / Line 17: @@
 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).
+<!--Modules-->
-== Available versions==
+==Required Modules==
-* 6.1 release
+[[Modules|modules documentation]]
-* 6.1-20110830 CVS - Developmental snapshot
+===Serial===
-* 6.1-20120110 CVS - Developmental snapshot
+*{{#var:app}}
-* 6.1-20120117 CVS - Developmental snapshot
+==System Variables==
-* 7.0.1.22 (default)
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-<!-- -->
-{{#if: {{#var: mod}}|==Execution Environment and Modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 * HPC_WGS_BIN - executable directory
 {{#if: {{#var: exe}}|==How To Run==
@@ Line 51: / Line 31: @@
 {{#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 58: / Line 38: @@
 *'''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__
+=Validation=
+* Validated 4/5/2018

Difference between revisions of "Wgs"