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bio-workflows-methylation-pipeline

Process bisulfite sequencing FASTQ data into differentially methylated regions.

Updated Mar 30, 2026
Search Tags:#genomics#methylation#dmr#bisulfite#methylkit#bs-seq
One-click install
npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-workflows-methylation-pipeline
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-workflows-methylation-pipeline
Source: https://github.com/ya-way/cytoclaw-skills/tree/main/workspace/skills/bio-wf-methylation-pipeline
Command: npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-workflows-methylation-pipeline

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This end-to-end bisulfite sequencing workflow automates the analysis from raw FASTQ reads to identified differentially methylated regions, reducing manual steps and improving reproducibility.

Core Features & Use Cases

  • Align bisulfite reads with Bismark and call methylation
  • Analyze methylation with methylKit to identify DMRs and annotate genomic features
  • Use cases include whole-genome bisulfite sequencing (WGBS) and RRBS data to compare conditions and generate methylation reports

Quick Start

Run the methylation pipeline on bisulfite sequencing data to generate DMR results.

Frequently Asked Questions about bio-workflows-methylation-pipeline

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

FAQPage Schema
How do I analyze bisulfite sequencing data from FASTQ to differentially methylated regions?▼

The pipeline processes WGBS and RRBS data by aligning bisulfite reads with Bismark, calling methylation, and using methylKit to identify differentially methylated regions and annotate genomic features.

Can I use this workflow for both WGBS and RRBS data?▼

Yes, the workflow supports both whole-genome bisulfite sequencing (WGBS) and RRBS data, aligning reads with Bismark and using methylKit to compare conditions and generate methylation reports.

Do I need Bismark and methylKit installed to identify DMRs?▼

Yes, identifying DMRs requires an R/Python environment with Bismark, methylKit, and Genomation-compatible tools installed to perform alignment, methylation calling, and analysis.

What is the best way to automate methylation calling and DMR annotation?▼

The best way is to use an end-to-end bisulfite sequencing workflow that automates methylation calling and DMR annotation, reducing manual steps and improving reproducibility from FASTQ to results.

How does methylKit integrate with Bismark output for methylation analysis?▼

methylKit integrates with Bismark output by taking aligned bisulfite reads and methylation calls to perform statistical analysis, identify differentially methylated regions, and annotate genomic features.

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