hic

What problem does it solve?

This Skill streamlines Hi-C sequencing analysis by turning raw chromosome conformation capture data into standardized, reproducible outputs without requiring users to memorize pipeline flags.

Core Features & Use Cases

• End-to-End Hi-C Processing: Runs the nf-core/hic pipeline for alignment, valid pair detection, contact map generation, and downstream analysis.
• Protocol Flexibility: Supports common Hi-C variants such as restriction-enzyme digestion and DNase Hi-C, along with optional skipping of map, TAD, compartment, and MultiQC steps.
• Reproducible Execution: Uses a validated samplesheet and parameter schema, records provenance, and preserves versioned outputs for reliable re-runs and handoffs.
• Use Case: A bioinformatics analyst can point the Skill at a samplesheet, choose the reference genome or custom indices, and produce a complete Hi-C results directory for review.

Quick Start

Use the hic skill to analyze your Hi-C samplesheet and save the validated results into the output directory you specify.