├── .DS_Store ├── LICENSE ├── README.md ├── annotated_gene_report.png ├── annotated_gene_report.tsv ├── example_annotatedAMRreport.tsv ├── example_data_kleb ├── ERR257656_amrFinderPlusOutput.tsv ├── EuSCAPE_DE047_amrFinderPlusOutput.tsv ├── EuSCAPE_HR089_amrFinderPlusOutput.tsv ├── INF014_amrFinderPlusOutput.tsv └── SGH10_amrFinderPlusOutput.tsv ├── example_dict_kleb ├── Kleb_local_dict.tsv ├── Kleb_local_drugs_to_report.tsv └── make_Kleb_local_dict.Rmd ├── genome_report.pdf ├── genome_report.png ├── genome_report.rtf ├── organism_specific_rules.png ├── organism_specific_rules.tsv ├── parse_amrfinder.py └── pipeline.png /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/katholt/AMRrules/HEAD/.DS_Store -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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