Overview

This Nextflow pipeline is designed for the analysis of Twist NGS Methylation data, including quality control, alignment, methylation calling, differential methylation analysis, and post-processing. It integrates various tools and custom scripts to provide a comprehensive analysis workflow.

Scehmatic of the pipeline

Features

Step	Workflow
Generate Reference Genome Index (optional)	Bismark
Raw data QC	FastQC
Adapter sequence trimming	Trim Galore
Align Reads	Bismark (bowtie2)
Deduplicate Alignments	Bismark
Sort and indexing	Samtools
Extract Methylation Calls	Bismark
Sample Report	Bismark
Summary Report	Bismark
Alignment QC	Qualimap
QC Reporting	MultiQC
Differential Methylation Analysis	EdgeR/MethylKit
Post processing	ggplot2
GO analysis	Gene Ontology