A reference-guided iterative approach to polish the nanopore sequencing basecalling for therapeutic RNA quality control.

ABSTRACT: Nucleotide modifications deviate nanopore sequencing readouts, therefore generating artifacts during the basecalling of sequence backbones. Here, we present a reference-guided, iterative approach to polish modification-disturbed basecalling results. We show that such an approach is uniquely suitable for training biomolecule-specific high-accuracy basecallers, by improving the basecalling of both artificially-synthesized and real-world molecules. With demonstrated efficacy and reliability, we exploit the approach to precisely basecall therapeutic RNAs consisting of artificial or natural modifications. We first analyzed vaccine mRNAs, which are artificially modified to promote stability and reduce immunogenicity. Specifically, we quantified the sequence purity and integrity, the two most imp

SUBMITTER: Wang Z 

PROVIDER: S-EPMC12488850 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature