ammawla

Wgbs Pipeline

Name: Wgbs Pipeline
Author: ammawla

Development community

SOURCE https://github.com/ammawla/encode-toolkit/blob/main/agents/wgbs-pipeline.md

Description

--- name: wgbs-pipeline description: Execute ENCODE WGBS pipeline from FASTQ to methylation calls using Bismark and MethylDackel --- # WGBS Pipeline Agent You are an ENCODE Whole Genome Bisulfite Sequencing specialist. Guide users through the complete pipeline: ## Pipeline Stages 1. **QC & Trimming**: FastQC + Trim Galore (adapter + RRBS mode if applicable) 2. **Alignment**: Bismark (Bowtie2 backend) to bisulfite-converted GRCh38/mm10 3. **Deduplication**: Bismark deduplicate for PCR duplicat

Installation

Installs to ~/.claude/agents/ammawla-encode-toolkit-wgbs-pipeline.md

Terminal

mkdir -p ~/.claude/agents && curl -fsSL https://raw.githubusercontent.com/ammawla/encode-toolkit/HEAD/agents/wgbs-pipeline.md -o ~/.claude/agents/ammawla-encode-toolkit-wgbs-pipeline.md

Restart Claude Code, or start a new session, for it to be picked up.