Difference between revisions of "ARC"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|arc}} | |{{#vardefine:app|arc}} | ||
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of 1) reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together and 2) reduce reference bias as compared to mapping based approaches. The software is designed to work in situations where a whole-genome assembly is not the objective, but rather when the researcher wishes to assemble discreet 'targets' contained within next-generation shotgun sequence data. ARC decomplexifies the traditionally difficult problem of assembly by subsetting the reads into small, manageable pieces which can then be assembled quickly and efficiently. Applications include those in which the researcher wishes to de novo assemble specific content and a set of semi-similar reference targets is available to initialize the assembly process. | + | ARC is a pipeline which facilitates iterative, reference guided ''de novo'' assemblies with the intent of 1) reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together and 2) reduce reference bias as compared to mapping based approaches. The software is designed to work in situations where a whole-genome assembly is not the objective, but rather when the researcher wishes to assemble discreet 'targets' contained within next-generation shotgun sequence data. ARC decomplexifies the traditionally difficult problem of assembly by subsetting the reads into small, manageable pieces which can then be assembled quickly and efficiently. Applications include those in which the researcher wishes to de novo assemble specific content and a set of semi-similar reference targets is available to initialize the assembly process. |
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | In preparing your ARC_config.txt file, be careful in how things are named. Do not start a non-numerical parameter with a number. ARC checks if the parameter starts with a number, and if it does, assumes the whole parameter is a number and tries to convert to integer. | |
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| + | For example a reference file that is named 5_genes.fasta would throw an error because ARC sees the 5, assumes the parameter is a number and tries to convert "5_genes.fata" into an integer. | ||
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|}} | |}} | ||
<!--PBS scripts--> | <!--PBS scripts--> | ||
Latest revision as of 14:32, 12 August 2022
Description
ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of 1) reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together and 2) reduce reference bias as compared to mapping based approaches. The software is designed to work in situations where a whole-genome assembly is not the objective, but rather when the researcher wishes to assemble discreet 'targets' contained within next-generation shotgun sequence data. ARC decomplexifies the traditionally difficult problem of assembly by subsetting the reads into small, manageable pieces which can then be assembled quickly and efficiently. Applications include those in which the researcher wishes to de novo assemble specific content and a set of semi-similar reference targets is available to initialize the assembly process.
Environment Modules
Run module spider arc to find out what environment modules are available for this application.
System Variables
- HPC_ARC_DIR - installation directory
Additional Information
In preparing your ARC_config.txt file, be careful in how things are named. Do not start a non-numerical parameter with a number. ARC checks if the parameter starts with a number, and if it does, assumes the whole parameter is a number and tries to convert to integer.
For example a reference file that is named 5_genes.fasta would throw an error because ARC sees the 5, assumes the parameter is a number and tries to convert "5_genes.fata" into an integer.