Difference between revisions of "Oases"
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Moskalenko (talk | contribs) (Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:BioinformaticsCategory:NGS <!-- ######## Template Configuration ######## --> <!--Edit definitions of the variab...") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Assembly]] |
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| − | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|oases}} | |{{#vardefine:app|oases}} | ||
|{{#vardefine:url|http://www.ebi.ac.uk/~zerbino/oases/}} | |{{#vardefine:url|http://www.ebi.ac.uk/~zerbino/oases/}} | ||
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|{{#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}}}}|}} | + | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} |
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Oases is a de novo transcriptome assembler designed to produce transcripts | Oases is a de novo transcriptome assembler designed to produce transcripts | ||
from short read sequencing technologies, such as Illumina, SOLiD, or 454 in | from short read sequencing technologies, such as Illumina, SOLiD, or 454 in | ||
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for Molecular Genomics) and Daniel Zerbino (previously at the European | for Molecular Genomics) and Daniel Zerbino (previously at the European | ||
Bioinformatics Institute (EMBL-EBI), now at UC Santa Cruz). | Bioinformatics Institute (EMBL-EBI), now at UC Santa Cruz). | ||
| − | <!-- | + | <!--Modules--> |
| − | + | ==Environment Modules== | |
| − | == | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
| − | + | ==System Variables== | |
| − | < | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
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* HPC_OASES_BIN | * HPC_OASES_BIN | ||
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{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
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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 | + | {{#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 17:25, 19 August 2022
Description
Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. It was developed by Marcel Schulz (MPI for Molecular Genomics) and Daniel Zerbino (previously at the European Bioinformatics Institute (EMBL-EBI), now at UC Santa Cruz).
Environment Modules
Run module spider oases to find out what environment modules are available for this application.
System Variables
- HPC_OASES_DIR - installation directory
- HPC_OASES_BIN