pipeline-wgbs

Process WGBS FASTQ files into ENCODE-compliant methylation calls.

26|5|Updated Mar 8, 2026

Search Tags:#bioinformatics #nextflow #methylation #epigenomics #WGBS #bisulfite

Ready to run

npx skills add https://github.com/ammawla/encode-toolkit --skill pipeline-wgbs

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pipeline-wgbs
Source: https://github.com/ammawla/encode-toolkit/tree/main/plugin/skills/pipeline-wgbs
Command: npx skills add https://github.com/ammawla/encode-toolkit --skill pipeline-wgbs

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires samtools, bwa, bismark, MethylDackel, fastqc, multiqc, picard, trim_galore, and includes scripts (resource) and references (resource) components.

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.

Frequently Asked Questions about pipeline-wgbs

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I process raw WGBS FASTQ files for methylation analysis?▼

To process raw WGBS FASTQ files, you perform adapter trimming, bisulfite-aware alignment, deduplication, and methylation extraction to generate high-confidence calls. This pipeline handles these steps end-to-end to produce bedMethyl files for downstream epigenomic analysis.

What quality control metrics are needed for whole-genome bisulfite sequencing data?▼

Whole-genome bisulfite sequencing quality control requires evaluating bisulfite conversion rates, coverage, mapping, and duplication metrics. This pipeline ensures these metrics meet ENCODE standards, providing standardized QC reports through MultiQC for reliable epigenomic research.

Does this methylation analysis pipeline support Bismark for bisulfite alignment?▼

Yes, this methylation analysis pipeline supports Bismark for bisulfite-aware alignment. It integrates Bismark alongside BWA, Trim Galore, and Picard to execute the core processing steps required for comprehensive whole-genome bisulfite sequencing analysis.

What is the best way to ensure WGBS methylation calls adhere to ENCODE standards?▼

The best way to ensure WGBS methylation calls adhere to ENCODE standards is by using a standardized processing pipeline with built-in QC metrics. This approach validates bisulfite conversion rates and alignment quality to guarantee high-confidence epigenomic results.

Can I use Nextflow to automate end-to-end WGBS data processing?▼

Yes, you can use Nextflow to automate end-to-end WGBS data processing. This pipeline leverages Nextflow to orchestrate the entire workflow, from adapter trimming and bisulfite-aware alignment to methylation extraction and quality assessment.