A whole-genome sequencing dataset of nanopore raw signals for bacterial genotyping and methylation analysis

This dataset comprises raw signal data from a multicenter study evaluating the accuracy of bacterial whole-genome genotyping using Oxford Nanopore long-read sequencing. The raw data comprises 79 isolates across six bacterial species, including 12 triplicates from three different laboratories (totalling ~1.4 TB of data). Sequencing was conducted on the latest R10.4.1 flow cells with V14 chemistry, producing on average 16 gigabases per flow cell. The generated raw ion current signals retain information beyond nucleotide sequences, supporting in-depth reanalysis for nucleotide modifications, resistance genes, and bacterial strain differentiation. The dataset enables re-basecalling with future models to keep up with the newest developments, e.g. to mitigate methylation-based calling errors, enhancing the reliability of SNP profiling and cgMLST analyses crucial for genomic surveillance. By sharing this raw signal data, accompanied by additional phenotypic resistance-data and an extensive quality control pipeline, we aim to advance reproducibility, support error correction studies and the continued development of bioinformatics tools, and encourage sharing raw data for broader genomic and epigenetic investigations as general best practice.