Difference between revisions of "RGI"
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|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
<!--Configuration--> | <!--Configuration--> | ||
Latest revision as of 21:24, 6 December 2019
Description
This application is used to predict resistome(s) from protein or nucleotide data based on homology and SNP models. The application uses reference data from the Comprehensive Antibiotic Resistance Database (CARD).
RGI analyses can be performed via the CARD website RGI portal, via use of a Galaxy wrapper for the Galaxy platform, or alternatively you can Install RGI from Conda or `Run RGI from Docker`_. The instructions below discuss use of RGI at the command line, following a general overview of how RGI works for genomes, genome assemblies, proteomes, and metagenomic sequencing.
Environment Modules
Run module spider rgi to find out what environment modules are available for this application.
System Variables
- HPC_RGI_DIR - installation directory
- HPC_RGI_BIN - executable directory
Citation
If you publish research that uses rgi you have to cite it as follows: