Antimicrobial resistance

AMRFinderPlus

The results of running AMRFinderPlus for AllTheBacteria are available on OSF in the AMRFinderPlus component.

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.

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 current version of the AMRFinderPlus results were run using a Nextflow pipeline found here using AMRFinderPlus version v4.2.5 with database 2025-12.03.1.

Genomes were matched to the organism available in AMRFinderPlus where possible; a table linking each ATB species to its corresponding AMRFinderPlus species can be found here.

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 (no AMRFinderPlus hits detected).

We also include a copy of the amrfinder database we used in each database sub-folder.

amrfinderplus.parquet is a Parquet database file for use with the ATB command line interface. It includes two additional columns, genus and species which can be used for filtering.

Updates to AMR calls

The dataset will be updated at least yearly with newer version of AMRFinderPlus and its database; therefore, 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.

Previous AMRFinderPlus results

AMRFinderPlus v3.12.8

This workflow was run on the original v0.2 and 2024-08 sets of genomes. It used AMRFinderPlus v3.12.8, and details are below:

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.

We have included sub-folders of the results broken down by the AllTheBacteria release, useful if you just want the results for a new incremental release.

If you want to do this and have any questions or need some help, please contact Daniel Anderson.