Benchmarking Illumina and Oxford Nanopore Technologies (ONT) sequencing platforms for whole genome sequencing of bacterial genomes and use in clinical microbiology

Combining Illumina and ONT technologies yielded optimal bacterial genome sequencing results, leveraging the high accuracy of short reads and improved contiguity of ONT long reads. The HAC and SUP ONT models with Dorado notably enhance genome assembly annotation and resolution of complex regions, although species-specific issues, likely due to repeat regions and base modifications, remain challenging even in SUP model with Dorado. Hybrid approaches currently offer the most comprehensive and accurate genome assemblies for clinical microbiology. For reliable cgMLST even using the most recent ONT methods, resolution must be assessed on a species-by-species basis.