bio-workflows-methylation-pipeline

npx skills add majiayu000/claude-skill-registry --skill methylation-pipeline-gptomics-bioskills-2 --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# Methylation Pipeline Complete workflow from bisulfite sequencing FASTQ to differentially methylated regions. ## Workflow Overview ``` FASTQ files | v [1. QC & Trimming] -----> fastp/Trim Galore | v [2. Alignment] ---------> Bismark | v [3. Deduplication] -----> deduplicate_bismark | v [4. Methylation Calling] -> bismark_methylation_extractor | v [5. Analysis] -----------> methylKit (R) | v [6. DMR Detection] ------> methylKit/DSS | v Differentially methylated regions ``` ## Primary Path: Bismark + methylKit ### Step 1: Quality Control ```bash # Trim Galore recommended for bisulfite data (handles adapter bias) trim_galore --paired --fastqc \ -o trimmed/ \ sample_R1.fastq.gz sample_R2.fastq.gz # Or fastp with conservative settings fastp -i sample_R1.fastq.gz -I sample_R2.fastq.gz \ -o trimmed/sample_R1.fq.gz -O trimmed/sample_R2.fq.gz \ --detect_adapter_for_pe \ --qualified_quality_phred 20 \ --length_required 35 \ --html qc/sample_fastp.html ``` ### Step 2: Bismark Alignment ```bash # Prepare genome (once) bismark_genome_preparation --bowtie2 genome/ # Align bismark --genome genome/ \ -1 trimmed/sample_R1_val_1.fq.gz \ -2 trimmed/sample_R2_val_2.fq.gz \ -o aligned/ \ --parallel 4

Trim Galore recommended for bisulfite data (handles adapter bias)
trim_galore --paired --fastqc \
sample_R1.fastq.gz sample_R2.fastq.gz
Or fastp with conservative settings
fastp -i sample_R1.fastq.gz -I sample_R2.fastq.gz \
Prepare genome (once)
bismark_genome_preparation --bowtie2 genome/
Align
bismark --genome genome/ \
deduplicate_bismark \