These findings show that Nanopore data is now accurate enough, practical and ready for further integration into clinical settings. Massive thankyou to @nenadmacesic.bsky.social, @yekwah.bsky.social, @katholt.bsky.social and all others who contributed to this project! /5

We provide specific recommendations for sequencing depth, basecalling model and analysis methods depending on the resources available and clinical context of the user. Analysis time is negligible, the biggest time savings come from choosing your basecalling model and depth requirements /4

We found modern ONT data (R10.4.1, Dorado SUP) to generate perfect MLST profiles and AMR allelic variant profiles, ~99.5% cgMLST profiles and cgSNP profiles highly concordant with traditional Illumina methods /3

Nanopore data has come a long way the last few years, and offers users a huge amount of flexibility in how they want to generate data. We took all combinations of sequencing chemistry, basecalling, depth & assembly status from 3 Gram-negative species groups and compared to hybrid gold standards /2