Scripts to support AMR tool benchmarking study
run-select-final.sh is the pipeline runner script that calls the individual pipeline components from within run-rgi.
run-rgi/ directory contains the prototype scripts used to run the various components of the CARD RGI-based pipeline for mNGS and WGS data with species-calling.
notebooks/ directory contains the jupyter notebooks that were used to process the outputs of the CARD RGI-based pipeline and generate combined tables for UXR.
run-tools contains scripts to run each individual tool and a wrapper to run all the tools given input files. These files are currently dependent on a particular set-up directory structure and will be difficult to run automatically.