What it does

hAMRonization parses multiple Antimicrobial Resistance Analysis Reports from disparate antimicrobial resistance gene detection tools into a single unified format.

This is an implementation of the hAMRonization AMR detection specification scheme which supports gene presence/absence resistance and mutational resistance (if supported by the underlying tool).

Inputs

Report or output of an antimicrobial resistance gene detection tool:

• abricate: abricate's output report i.e., OUTPUT.tsv
• amrfinderplus: amrfinderplus's output report i.e., OUTPUT.tsv
• ariba: ariba's output report i.e., OUTDIR/OUTPUT.tsv
• rgi: rgi's output report i.e., OUTPUT.txt or OUTPUT_bwtoutput.gene_mapping_data.txt
• resfinder: resfinder's output report i.e., data_resfinder.json
• resfinder4: resfinder4's tabular output report i.e., ResFinder_results_tab.txt
• srax: srax's output report i.e., sraX_detected_ARGs.tsv
• deeparg: deeparg's output report i.e., OUTDIR/OUTPUT.mapping.ARG
• kmerresistance: kmerresistance's output report i.e., OUTPUT.KmerRes
• srst2: srst2's output report i.e., OUTPUT_srst2_report.tsv
• staramr: staramr's output report i.e., resfinder.tsv
• csstar: csstar's output report i.e., OUTPUT.tsv
• amrplusplus: amrplusplus's output report i.e., gene.tsv
• resfams: resfams's output report i.e., resfams.tblout
• groot: groot's output report i.e., OUTPUT.tsv (from groot report)

More: https://github.com/pha4ge/hAMRonization/#usage