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

Authors

Liu, X., Ding, Q., Shao, Y., GUO, Z., Ni, Y., Fan, L., Yang, Y., Yang, M., Li, R.

Abstract

Nanopore sequencing underpins bacterial genomics and epigenomics, with Oxford Nanopore Technologies (ONT) leading. We benchmarked BGI's CycloneSEQ against ONT using matched whole-genome shotgun (WGS) and methylation-free whole-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-read polishing, CycloneSEQ assemblies achieved around 100% completeness with ~1 indel per 100 Kbp. For epigenomics, strand-specific basecalling errors enabled de novo discovery of 12 methylation motifs, and we introduce two CycloneSEQ-compatible signal-to-reference alignment strategies that permit signal comparison-based methylation detection. Beyond a single instrument, these results argue for a unified, cross-platform nanopore toolchain in which models, formats, and workflows interoperate from raw signal to accurate assemblies and methylomes.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 16 Jan 2026.

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