hic

Process Hi-C sequencing data into standardized analysis outputs.

1|Updated Jun 19, 2026

Search Tags:#provenance #bioinformatics #genomics #nf-core #hic #chromosome conformation #contact maps

Ready to run

npx skills add https://github.com/danilomonge/nf-claw --skill hic

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: hic
Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/hic
Command: npx skills add https://github.com/danilomonge/nf-claw --skill hic

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

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.

Frequently Asked Questions about hic

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I process raw Hi-C sequencing data into contact maps?▼

You can generate Hi-C contact maps by providing a validated CSV samplesheet, which triggers paired-end alignment, valid pair detection, and standardized contact map generation without manual pipeline flags.

Does this Hi-C analysis workflow support DNase Hi-C and restriction enzyme digestion protocols?▼

Yes, the workflow supports both restriction-enzyme digestion and DNase Hi-C protocols, allowing you to process diverse chromosome conformation capture datasets for contact map generation.

How do I call TADs and compartments from chromosome conformation capture data?▼

To call TADs and compartments from chromosome conformation capture data, run the downstream analysis steps included in the pipeline, with options to skip TAD, compartment, or MultiQC generation as needed.

How do I ensure reproducible results when running chromosome conformation capture pipelines?▼

Reproducible chromosome conformation capture results are enforced through nf-schema parameter validation, required CSV samplesheet inputs, versioned provenance tracking, and standardized output contracts for reliable re-runs.

Can I use custom reference genome indices for nf-core Hi-C alignment?▼

Yes, you can specify a reference genome or provide custom indices when running the Hi-C pipeline, allowing the workflow to align paired-end reads against your desired reference assembly.

What input format is required for running chromosome conformation capture analysis?▼

A validated CSV samplesheet is required as the input format for chromosome conformation capture analysis, undergoing nf-schema parameter validation to ensure standardized and reproducible processing outputs.