Scaffolding - Usage Guide

Scaffolding - Usage Guide

Overview

Scaffolding orders and orients contigs into chromosome-level assemblies using Hi-C proximity ligation data to infer long-range contacts.

Prerequisites

# YaHS
conda install -c bioconda yahs

# 3D-DNA
git clone https://github.com/aidenlab/3d-dna.git

# SALSA2
conda install -c bioconda salsa2

# Juicer tools
wget https://github.com/aidenlab/juicer/releases/download/v2.0/juicer_tools.2.0.jar

Quick Start

Tell your AI agent what you want to do:

• "Scaffold my draft assembly using Hi-C data with YaHS"
• "Generate a contact map for Juicebox visualization"
• "Create chromosome-level scaffolds from my contigs"

Example Prompts

Hi-C Scaffolding

"Scaffold my draft assembly using Hi-C data with YaHS" "Run 3D-DNA scaffolding with my Hi-C alignments" "Use SALSA2 to scaffold my contigs with proximity ligation data"

Visualization

"Generate a contact map for Juicebox visualization" "Create a .hic file from my scaffolded assembly"

Post-Scaffolding

"Fill gaps in scaffolds using long reads" "Validate my scaffolded assembly with BUSCO" "Check for telomeric sequences at scaffold ends"

What the Agent Will Do

1. Align Hi-C reads to draft assembly
2. Filter contacts and remove PCR duplicates
3. Run scaffolding tool (YaHS/3D-DNA/SALSA2)
4. Generate contact map for visualization
5. Provide statistics on scaffold N50 and chromosome count
6. Suggest manual curation if needed

Tips

• YaHS is recommended for most projects due to speed and accuracy
• Hi-C library quality is critical for scaffolding success
• Use Juicebox for manual inspection and curation of problem regions
• Telomere detection can validate chromosome completeness
• Gap-filling with long reads improves final assembly quality
• Draft assembly contiguity affects final chromosome assembly