Hi-C Scaffolding Nextflow Pipeline

A Nextflow pipeline for scaffolding genome assemblies using Hi-C reads with CHROMAP, YAHS, and Juicer Tools.

---

Table of Contents

• Introduction
• Quick Start
• Inputs
• Outputs
• Dependencies
• Configuration
  • Running Locally/Elsewhere
• Examples
• Troubleshooting
• References

---

Introduction

This pipeline scaffolds draft genome assemblies using Hi-C data in three steps:

1. Alignment: Hi-C reads are mapped to contigs using CHROMAP.
2. Scaffolding: Contigs are ordered/oriented using YAHS.
3. Visualization: Prepares files for manual curation in Juicebox.

---

Quick Start

nextflow run digenoma-lab/hic-scaffolding-nf \
    --contigs contigs.fa \
    --r1Reads hic_R1.fastq.gz \
    --r2Reads hic_R2.fastq.gz \
    -profile conda  # Use conda for dependencies

---

Inputs

Parameter	Format	Description
--contigs	FASTA	Draft assembly contigs.
--r1Reads	FASTQ(.gz)	Hi-C paired-end reads (R1).
--r2Reads	FASTQ(.gz)	Hi-C paired-end reads (R2).
--large	Boolean	Use this options for genomes > 4Gb

---

Outputs

Directory	Files	Description
out/chromap/	aligned.bam	Hi-C read alignments.
out/scaffolds/	yahs.out_scaffolds_final.fa	Scaffolded assembly (FASTA).
out/scaffolds/	yahs.out_scaffolds_final.agp	AGP file for scaffolding.
out/juicebox_input/	out_JBAT.hic	Juicebox-compatible Hi-C map.
out/juicebox_input/	out_JBAT.assembly	Assembly file for Juicebox.

---

Dependencies

• Core:
  • Nextflow (≥20.04.0)
  • CHROMAP (alignment)
  • YAHS (scaffolding)
  • Juicer Tools (visualization)

---

Configuration

Running Locally or on Other Clusters

1. Conda (recommended for CHROMAP/YAHS):

   -profile conda

Add custom configuration in nextflow.config:

params {
  juicer_tools_jar = "/path/to/juicer_tools.jar"
}
process {
    withName: 'PRINT_VERSIONS' {
        cpus = 1
        memory = 1.GB
    }
    
   withName: 'SAMTOOLS_FAIDX' {
        cpus = 1
        memory = 1.GB
    }

    withName: 'CHROMAP_INDEX' {
        cpus = 10
        memory = 100.GB
    }

    withName: 'CHROMAP_ALIGN' {
        cpus = 44
        memory = 100.GB
    }

    withName: 'YAHS_SCAFFOLD' {
        cpus = 10
        memory = 100.GB
    }


    withName: 'JUICER_PRE' {
        cpus = 10
        memory = 100.GB
    }

    withName: 'ASSEMBLY_STATS' {
        cpus = 1
        memory = 10.GB
    }

}

---

Examples

Basic Run

nextflow run hic-scaffolding-nf/main.nf \
    --contigs sl_female_ont_purge_r2.fasta \
    --r1Reads DDU_AAOSDF_4_1_HFYVJDSX7.UDI488_clean.fastq.gz \
    --r2Reads DDU_AAOSDF_4_2_HFYVJDSX7.UDI488_clean.fastq.gz \
    -profile uoh  # Example profile

---

Troubleshooting

• Missing files: Ensure all input paths are correct.
• Conda issues: Use -profile conda or install dependencies manually.
• Juicer Tools: Specify the JAR path with --juicer_tools_jar.

---

References

• CHROMAP
• YAHS
• Juicer Tools
• Nextflow Docs