When CycloneSEQ meets Oxford Nanopore Technologies: a performance comparison of contemporary nanopore DNA sequencing platforms

Nanopore sequencing underpins bacterial genomics and epigenomics, with Oxford Nanopore Technologies (ONT) leading. We benchmarked BGIs CycloneSEQ against ONT using matched whole{square}genome shotgun (WGS) and methylation{square}free whole{square}genome amplification (WGA) libraries across six bacteria. With the updated CycloneSEQ kit/basecaller, reads reached 96.0% accuracy (mode 97.7%), within 0.8% of ONT R10.4.1; homopolymer performance surpassed R9.4.1 and approached R10.4.1. Error spectra were shared across platforms and dominated by A and G substitutions, WGA controls implicated methylation as a major contributor. At 50-fold coverage plus short{square}read polishing, CycloneSEQ assemblies achieved around 100% completeness with [~]1 indel per 100 Kbp. For epigenomics, strand{square}specific basecalling errors enabled de novo discovery of 12 methylation motifs, and we introduce two CycloneSEQ{square}compatible signal{square}to{square}reference alignment strategies that permit signal comparison-based methylation detection. Beyond a single instrument, these results argue for a unified, cross{square}platform nanopore toolchain in which models, formats, and workflows interoperate from raw signal to accurate assemblies and methylomes.