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Running
abriTAMR runs AMRFinderPlus on a list of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.
abriTAMR accepts assemblies as input. Users should provide a tab-delimited file <isolate_id> <path_to_contigs>. For use in the context of MDU, a mdu_qc_checked.csv file should also be provided. This file should be comma-delimited and contain at a minimum columns for ,<ITEM_CODE>,<SPECIES_OBS>,<SPECIES_EXP>,<TEST_QC>
abriTAMR is implemented as part of MDU QC pipeline. It can also be run for MDU use as described below, with a comma-delimted mdu_qc_checked.csv file in the working directory.
When running abriTAMR for MDU use a positive control must be included
abriTAMR -c <input_file> -m
When running abriTAMR for MDU use, the output is an Excel file (MMS118.xlsx) with two tabs MMS118, MMS118 - passed QC partial is generated and emailed to MMDI.