pipeline-hiclisted

Execute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing Hi-C data, generating contact matrices, calling loops or TADs. Trigger on: Hi-C pipeline, chromatin conformation, contact matrix, loop calling, TAD detection, Juicer, HiCCUPS, 3D genome.
ammawla/encode-toolkit · ★ 35 · Data & Documents · score 79

Install: claude install-skill ammawla/encode-toolkit

# ENCODE Hi-C Pipeline: FASTQ to Contact Matrices and Loops ## When to Use - User wants to run a Hi-C processing pipeline from FASTQ to contact matrices and loop calls - User asks about "Hi-C pipeline", "contact matrix", "loop calling", "Juicer", "HiCCUPS", or "TAD detection" - User needs to process Hi-C data for 3D genome structure analysis - Example queries: "process my Hi-C FASTQs", "generate contact matrices from Hi-C", "call chromatin loops with HiCCUPS" Execute the ENCODE Hi-C pipeline for chromatin conformation capture data, producing multi-resolution contact matrices, loop calls, and compartment annotations. ## Pipeline Overview ``` FASTQ -> Trim -> BWA (per-mate) -> pairtools parse -> dedup -> .pairs | +------------+------------+ | | Juicer pre -> .hic cooler -> .mcool | | HiCCUPS loops Compartments ``` ### ENCODE Repository - **GitHub**: `ENCODE-DCC/hic-pipeline` - **Container**: `encodedcc/hic-pipeline` - **WDL**: Available for Cromwell execution - **This skill**: Nextflow DSL2 reimplementation for portability ## Core Tools and Versions | Tool | Version | Purpose | Citation | |-----