Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment.

ABSTRACT: Nanopore signal analysis enables detection of nucleotide modifications from native DNA and RNA sequencing, providing both accurate genetic/transcriptomic and epigenetic information without additional library preparation. Presently, only a limited set of modifications can be directly basecalled (e.g. 5-methylcytosine), while most others require exploratory methods that often begin with alignment of nanopore signal to a nucleotide reference. We present Uncalled4, a toolkit for nanopore signal alignment, analysis, and visualization. Uncalled4 features an efficient banded signal alignment algorithm, BAM signal alignment file format, statistics for comparing signal alignment methods, and a reproducible de novo training method for k-mer-based pore models, revealing potential errors in ONT

SUBMITTER: Kovaka S 

PROVIDER: S-EPMC10942365 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature