pipeline-wgbs

What problem does it solve?

This Skill enables users to process and analyze whole-genome bisulfite sequencing data for comprehensive methylation profiling, ensuring high-quality, standardized results.

Core Features & Use Cases

• Data Processing: Performs adapter trimming, bisulfite-aware alignment, duplicate removal, and methylation extraction for WGBS datasets.
• Quality Control: Ensures bisulfite conversion rates meet ENCODE standards and provides coverage, mapping, and duplication metrics.
• Use Case: Researchers can process raw WGBS FASTQ files to generate bedMethyl files for downstream epigenomic analysis, such as identifying methylation patterns or differentially methylated regions.

Quick Start

Run the WGBS pipeline on your FASTQ files with a command specifying input files and reference genome to obtain methylation calls compatible with ENCODE standards.