This is an incredibly relevant preprint. Your favourite pipeline and/or AMR gene database cannot be considered authoritative, but neither can others.
Explore the results interactively: arg-pipelines.big-data-biology.org
Project led by Juan Inda-Diaz with a great team across the whole SEARCHER Consortium!
This section highlights the difference in number of Antimicrobial Resistance Genes (ARGs) reported by each pipeline.
arg-pipelines.big-data-biology.org
The original authors of DeepARG to caution against using results marked as "multidrug" (such as *rpoB*) without experimental validation, but this is rarely done.
Our conclusions: no single pipeline should be treated as authoritative.
A constrained methodological pluralism, whereby multiple approaches are seen as valid, each with limitations communicated carefully is the most honest reflection of the state-of-the-art.
