Difference between revisions of "Maker"
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Moskalenko (talk | contribs) (Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:BiologyCategory:Genomics <!-- ######## Template Configuration ######## --> <!--Edit definitions of the variable...") |
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| − | [[Category:Software]][[Category:Biology]] | + | [[Category:Software]][[Category:Biology]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
| − | + | |{{#vardefine:app|maker}} | |
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| − | |{{#vardefine:app| | ||
|{{#vardefine:url|http://www.yandell-lab.org/software/maker.html}} | |{{#vardefine:url|http://www.yandell-lab.org/software/maker.html}} | ||
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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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{{#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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MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal and its outputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources. | MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal and its outputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources. | ||
| − | <!-- | + | <!--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_MAKER_BIN - executable directory. | * HPC_MAKER_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 | + | {{#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 18:20, 18 August 2022
Description
MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal and its outputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.
Environment Modules
Run module spider maker to find out what environment modules are available for this application.
System Variables
- HPC_MAKER_DIR - installation directory
- HPC_MAKER_BIN - executable directory.