DNAModAnnot

DNAModAnnot facilitates genome-wide detection, annotation, and visualization of DNA modifications (6-methyladenine (6mA) and 5-methylcytosine (5mC)) from long-read sequencing data (Pacific Biosciences, Oxford Nanopore Technologies) to produce nucleotide-resolution epigenetic maps.

Key Features:

• Modular Architecture: Supports analysis of DNA modification calls derived from PacBio kineticsTools and ONT DeepSignal to accommodate diverse long-read workflows.
• Genome-wide Analysis and Annotation: Performs genome-wide mapping of DNA modifications and integrates genomic annotation to contextualize modification sites.
• Comprehensive Filtering: Implements advanced filtering tailored to refine detection of modified bases and improve the quality of modification calls.
• Customized Visualization Functions: Generates specialized visualizations for describing and interpreting complex DNA modification patterns.

Scientific Applications:

• 6-methyladenine (6mA) Analysis: Applied to Paramecium tetraurelia to analyze 6mA distribution, revealing genome-wide patterns consistent with those observed in other ciliates.
• 5-methylcytosine (5mC) Analysis: Applied to human lymphoblastoid cells using ONT sequencing data to confirm known 5mC patterns.

Methodology:

Processes modification calls from PacBio kineticsTools and ONT DeepSignal on Pacific Biosciences and Oxford Nanopore long-read data, applies filtering and genomic annotation, and produces nucleotide-resolution maps and visualizations of 6mA and 5mC.