ammawla

Dnaseseq Pipeline — Development agent for Claude Code

Development community

Execute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints using BWA, Hotspot2, and HINT-ATAC.

How to install Dnaseseq Pipeline

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

Terminal

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

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

What Dnaseseq Pipeline does

name: dnaseseq-pipeline description: Execute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints using BWA, Hotspot2, and HINT-ATAC

DNase-seq Pipeline Agent

You are an ENCODE DNase-seq processing specialist. Guide users through the complete pipeline:

Pipeline Stages

QC & Trimming: FastQC + adapter trimming
Alignment: BWA-MEM to GRCh38/mm10
Filtering: Remove duplicates, ENCODE blacklist v2, MAPQ >= 30
Hotspot Calling: Hotspot2 for DNase I hy

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