A population-specific pangenome for Saudi Arabia

Saudi Pangenome Analysis Pipeline

Overview

This repository contains workflows and data for constructing pangenomes from Saudi population genomic data using the minigraph-cactus pipeline. The workflows are implemented using Common Workflow Language (CWL), enabling reproducible and portable execution across different computing environments.

Background

Minigraph-Cactus Pipeline

Minigraph-cactus is a state-of-the-art pipeline that combines the efficiency of minigraph with the accuracy of Progressive Cactus for constructing pangenomes. This hybrid approach offers several advantages:

• Scalable construction of genome graphs from multiple assemblies
• Preservation of structural variants and complex genomic regions
• Efficient handling of large-scale genomic data
• Integration of both reference-based and reference-free approaches

The pipeline first uses minigraph to create initial graphs, followed by Progressive Cactus's sophisticated algorithms for multiple genome alignment, resulting in high-quality pangenome representations.

Common Workflow Language (CWL)

CWL is a specification for describing analysis workflows and tools. Its key features include:

• Platform independence
• Explicit declaration of dependencies
• Built-in support for Docker/container technologies
• Scalability from single workstations to HPC environments
• Clear separation of tools from the workflow logic

Workflows

Installation

Prerequisites

You need to install Docker or Singularity.

# Install required software
pip install cwltool

Repository Setup

git clone https://github.com/bio-ontology-research-group/pangenome

Usage

DeepVariant workflow

cwl-runner variant-calling/main-vg.cwl inputs.yml

Configuration

Create a YAML file with your inputs:

graph:
  class: File
  location: reference/ksa_hg38.gbz
reads1:
  class: File
  location: input/sample_R1.fastq.gz
reads2:
  class: File
  location: input/sample_R2.fastq.gz
hapl:
  class: File
  location: reference/ksa_hg38.hapl
ref_prefix: GRCh38
model_type: WGS
ref:
  class: File
  location: reference/hg38.fa
  secondaryFiles:
    - class: File
      location: reference/hg38.fa.fai
output_cram: aligned_reads.cram
output_vcf: sample.vcf
output_gvcf: sample.gvcf

Output Files

• aligned_reads.cram: Alignment against GRCh38
• sample.gvcf: Genomic VCF
• sample.vcf: Variant calls

Citation

If you use this pipeline in your research, please cite:

License

The data is available under CC0

Contact

Please create GitHub issues if you encounter any problems.