Correcting modification-mediated errors in nanopore sequencing by nucleotide demodification and reference-based correction.

ABSTRACT: The accuracy of Oxford Nanopore Technology (ONT) sequencing has significantly improved thanks to new flowcells, sequencing kits, and basecalling algorithms. However, novel modification types untrained in the basecalling models can seriously reduce the quality. Here we reports a set of ONT-sequenced genomes with unexpected low quality due to novel modification types. Demodification by whole-genome amplification significantly improved the quality but lost the epigenome. We also developed a reference-based method, Modpolish, for correcting modification-mediated errors while retaining the epigenome when a sufficient number of closely-related genomes is publicly available (default: top 20 genomes with at least 95% identity). Modpolish not only significantly improved the quality of in-house sequ

SUBMITTER: Chiou CS 

PROVIDER: S-EPMC10687267 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature