... or so the authors* claim in this paper:
Hall MB, Wick RR, Judd LM, Nguyen AN, Steinig EJ, Xie O, et al. Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data. Weigel D, editor. eLife. 2024;13: RP98300. doi:[10.7554/eLife.98300](https://doi.org/10.7554/eLife.98300)
This important study shows how a combination of the latest generation of Oxford Nanopore Technology long reads with state-of-the art variant callers enables bacterial variant discovery at an accuracy that matches or exceeds the current "gold standard" with short reads. The work thus heralds a new era, in which Illumina short-read sequencing no longer rules supreme. [Source: publisher's assessment, my emphasis.]
*) Including bioinformatics superheroes Ryan Wick and Torsten Seemann :)
Cheers Marco
PS: hope to see you all at the CoP meeting in 2 hours: https://dtudk.zoom.us/j/68365887835