This pipeline enables in-depth methylation analysis using base-resolution modification data. It processes raw or aligned ONT sequencing data, precomputed modification calls files, or methylation microarray data to quantify methylation rates across the genome and detect biologically meaningful differences between sample groups.

  • Input:

    • Raw/aligned sequencing data, modification tags (calls.tsv) files, or methylation microarray (idat) files

    • Sample group definitions metadatafor differential analysis

  • Output:

    • Per-base/probe methylation frequencies (5mC/5hmC)

    • Aggregated methylation summary tables per gene, CpG island, or DMR

    • Statistical testing of differential methylation between groups

    • Optional region-level output in BED or bigWig format for browser visualization

This analysis is ideal for detecting epigenetic biomarkers, understanding regulatory dynamics, or comparing methylation landscapes across tissues, treatments, or conditions.