Dear all,
Oh no, not another tool with an AMRwkward name! Wasn't hAMRonization enough already? (Try typing it if you disagree.)
But anyway, this looks like a valuable initiative:
Strepis N, Dollee D, Vrins D, Vanneste K, Bogaerts B, Carrillo C, et al. BenchAMRking: a Galaxy-based platform for illustrating the major issues associated with current antimicrobial resistance (AMR) gene prediction workflows. BMC Genomics. 2025;26: 27. doi:10.1186/s12864-024-11158-5. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-11158-5
I was a bit underwhelmed by the four currently included workflows (see: https://erasmusmc-bioinformatics.github.io/benchAMRking/), of which two are Salmonella-only, one Ecoli-only, and one multi-species (abritAMR), but things can grow from here.
How does it relate to hARMonization_workflow, which incorporates 18 AMR tools? BenchAMRking aims at validating AMR workflows for clinical and public health use, against a "gold standard" reference. hAMRonization_workflow was set up primarily to have a testing ground for hAMRonization, the tool to convert output from any AMR tool into a common format.
As its maintainer (Finlay Maguire) said, the workflow is almost too brittle to maintain. But how else will you test hAMRonization, manually run 18 tools over a dozen inputs?!
I recently submitted a bunch of patches to bring hAMRonization up to date with the latest tool versions. I also managed to upgrade hAMRonization_workflow to use all the latest tool versions.
Give it a try if you're up for it: https://github.com/pha4ge/hAMRonization_workflow. It installs with a simple "conda env create". Prepare for a long wait on the first run, while it installs all tools and databases. Subsequent runs are quick: it takes ~10mn on my laptop to run all 18 tools on an isolate.
Best wishes, AMRco ;-)