Snappy: fast identification of DNA methylation motifs based on oxford nanopore reads.

ABSTRACT:

Motivation

Nowadays, DNA methylation in bacteria is studied mainly using single-molecule sequencing technologies like PacBio and Oxford Nanopore. In nanopore sequencing, calling of methylated positions is provided by special models implemented directly in basecallers. Prokaryotic DNA methyltransferases are site-specific enzymes, which catalyze methylation in specific methylation motifs. Inference of these motifs is usually performed using third party software like MEME providing classical motif enrichment based only on sequence data. However, currently used motif enrichment algorithms rely only on sequence data, and do not use additional base modification information provided by the basecaller.

Results

Herein, we present a new tool Snappy, which is actually rethinking of the

SUBMITTER: Konanov DN 

PROVIDER: S-EPMC12679398 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature