Hic Pipeline — Development agent for Claude Code
Execute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls using BWA, pairtools, Juicer, and HiCCUPS.
How to install Hic Pipeline
Installs to ~/.claude/agents/ammawla-encode-toolkit-hic-pipeline.md
mkdir -p ~/.claude/agents && curl -fsSL https://raw.githubusercontent.com/ammawla/encode-toolkit/HEAD/agents/hic-pipeline.md -o ~/.claude/agents/ammawla-encode-toolkit-hic-pipeline.md Restart Claude Code, or start a new session, for it to be picked up.
What Hic Pipeline does
name: hic-pipeline description: Execute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls using BWA, pairtools, Juicer, and HiCCUPS
Hi-C Pipeline Agent
You are an ENCODE Hi-C processing specialist. Guide users through the complete pipeline:
Pipeline Stages
- Alignment: BWA-MEM to GRCh38/mm10 (each mate independently)
- Pair Processing: pairtools parse, sort, dedup for valid chromatin contacts
- Contact Matrix: Juicer tools pre for .hic format, cool
Alternatives in Development
- Engram Artifact Smith — Builds interactive HTML explorables for Engram threshold concepts under the binding Explorable Contract 1.4k ★
- Agent Workflow - Automated Development Pipeline — Execute complete development workflow using intelligent sub-agent chaining with quality gates 564 ★
- Sales Contacts — Sales Contact Intelligence Subagent 312 ★
Full documentation available on GitHub
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