Difference between revisions of "Newbler"
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| − | + | [[Category:Software]][[Category:Bioinformatics]][[Category:NGS]] | |
| + | {|<!--CONFIGURATION: REQUIRED--> | ||
| + | |{{#vardefine:app|newbler}} | ||
| + | |{{#vardefine:url|http://wiki.genomequest.com/index.php/Newbler_Assembler}} | ||
| + | <!--CONFIGURATION: OPTIONAL (1=ON)--> | ||
| + | |{{#vardefine:mod|1}} <!--MODULES - NOW REQUIRED--> | ||
| + | |{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice --> | ||
| + | |{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice --> | ||
| + | |{{#vardefine:exe|}} <!--RUNNING --> | ||
| + | |{{#vardefine:conf|}} <!--CONFIGS--> | ||
| + | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
| + | |{{#vardefine:policy|}} <!--POLICY--> | ||
| + | |{{#vardefine:testing|}} <!--TESTING/PROFILING--> | ||
| + | |{{#vardefine:faq|}} <!--FAQ--> | ||
| + | |{{#vardefine:citation|}} <!--CITATION--> | ||
| + | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
| + | |} | ||
| + | <!--BODY--> | ||
| + | <!--Description--> | ||
| + | {{#if: {{#var: url}}| | ||
| + | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | ||
| + | Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Sciences, a Roche Diagnostics company. | ||
| + | <!--Location--> | ||
| + | {{App_Location|app={{#var:app}}|{{#var:ver}}}} | ||
| + | <!--Versions--> | ||
| + | ==Available versions== | ||
| + | * 2.6 | ||
| + | <!--Modules--> | ||
| + | {{#if: {{#var: mod}}|==Running the application using modules== | ||
| + | {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | ||
| + | <!--Add additional HPC_FOO_BIN and other ENV VARIABLES below--> | ||
| + | * HPC_NEWBLER_BIN - executable directory | ||
| + | <!--Run--> | ||
| + | {{#if: {{#var: exe}}|==How To Run== | ||
| + | DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY | ||
| + | |}} | ||
| + | <!--Configuration--> | ||
| + | {{#if: {{#var: conf}}|==Configuration== | ||
| + | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details. | ||
| + | |}} | ||
| + | <!--PBS scripts--> | ||
| + | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
| + | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| + | <!--Policy--> | ||
| + | {{#if: {{#var: policy}}|==Usage policy== | ||
| + | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | ||
| + | |}} | ||
| + | <!--Performance--> | ||
| + | {{#if: {{#var: testing}}|==Performance== | ||
| + | DOUBLE_CLICK_TO_WRITE_PERFORMANCE_TESTING_RESULTS_HERE | ||
| + | |}} | ||
| + | <!--Faq--> | ||
| + | {{#if: {{#var: faq}}|==FAQ== | ||
| + | *'''Q:''' **'''A:'''|}} | ||
| + | <!--Citation--> | ||
| + | {{#if: {{#var: citation}}|==Citation== | ||
| + | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| + | DOUBLE_CLICK_TO_WRITE_CITATION_HERE | ||
| + | |}} | ||
| + | <!--Installation--> | ||
| + | {{#if: {{#var: installation}}|==Installation== | ||
| + | See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | ||
| + | __NOTOC____NOEDITSECTION__ | ||
Revision as of 21:18, 12 June 2012
Description
{{{name}}} website
Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Sciences, a Roche Diagnostics company.
Template:App Location
Available versions
- 2.6
Running the application using modules
To use newbler with the environment modules system at HPC the following commands are available:
Get module information for newbler:
$module spider newbler
Load the default application module:
$module load newbler
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_NEWBLER_DIR - directory where newbler is located.
- HPC_NEWBLER_BIN - executable directory