Correcting Modification-Mediated Errors in Nanopore Sequencing by Nucleotide Demodification and in silico Correction

The accuracy of Oxford Nanopore Technology (ONT) sequencing has significantly improved thanks to new flowcells, sequencing kits, and basecalling algorithms. However, novel modifications untrained in the basecalling models can seriously reduce the quality. This paper reports a set of ONT-sequenced genomes with unexpected low quality (∼Q30) due to extensive new modifications. Demodification by whole-genome amplification (WGA) significantly improved the quality of all genomes (∼Q50-60) while losing the epigenome. We developed a computational method, Modpolish, for correcting modification-mediated errors without WGA. Modpolish produced high-quality genomes and uncovered the underlying modification motifs without loss of epigenome. Our results suggested that novel modifications are prone to ONT errors, which are correctable by WGA or Modpolish without additional short-read sequencing.