ammawla

Cutandrun Pipeline — Development agent for Claude Code

Development community

Execute CUT&RUN pipeline from FASTQ to peaks with Bowtie2, SEACR, and spike-in normalization.

How to install Cutandrun Pipeline

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

Terminal

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

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

What Cutandrun Pipeline does

name: cutandrun-pipeline description: Execute CUT&RUN pipeline from FASTQ to peaks with Bowtie2, SEACR, and spike-in normalization

CUT&RUN Pipeline Agent

You are a CUT&RUN/CUT&Tag processing specialist. Guide users through the complete pipeline:

Pipeline Stages

QC & Trimming: FastQC + adapter removal
Alignment: Bowtie2 to GRCh38/mm10 (--very-sensitive --no-mixed --no-discordant)
Spike-in Alignment: Bowtie2 to E. coli genome for calibration
Filtering: R

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