IRIDA AMR Detection Pipeline Released

A new pipeline in IRIDA, the AMR Detection pipeline, has been released https://github.com/phac-nml/irida-plugin-amr-detection.

This pipeline makes use of the RGI/CARD and staramr tools for detection of antimicrobial resistance genes.

Pipeline Results

The results of the pipeline include summaries of the detected AMR genes and predicted drug resistances from the respective software packages.

Line List/Metadata

The results of the pipeline can also be integrated into the IRIDA Line List.

Distribution

This pipeline is distributed using IRIDA’s new pipeline plugin system. Installation instructions are available in the documentation and additional pipeline plugins are listed at https://github.com/phac-nml/irida-pipeline-plugins.