Antimicrobial resistance

AMRFinderPlus

The results of running AMRFinderPlus for AllTheBacteria are available on OSF in the AMRFinderPlus component. The results are organized into folders based on the version of amrfinder that was used, and sub-folders within these based on the amrfinder database version used. The dataset is frequently updated; therefore, we also include sub-folders of the results broken down by the AllTheBacteria release, useful if you just want the results for a new incremental release. The latest subfolder contains the most recent aggregated results of running on all samples in the AllTheBacteria dataset and can be found here: AMRFP_results.tsv.gz.

Each table of results has a matched status file. The status file indicates which samples we have run amrfinder on in the sample column, whether the run completed successfully (PASS), failed (FAIL), or is yet to be run (NOT DONE) in the status column. There is an additional column for any comments, such as indicating if the output of amrfinder was empty if no AMR determinants were identified. We also include a copy of the amrfinder database we used in each database sub-folder.

A Snakemake workflow to rerun this analysis can be found on the AllTheBacteria GitHub page here and modified fairly easily to use newer software or database versions. If you want to do this and have any questions or need some help, please contact Daniel Anderson.