laax 1.0.0

Local Ancestry Analysis in Crossbred Populations

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README

🧬 Local Ancestry Analysis Notebook

LAAX (Local Ancestry Analysis in Crossbred Populations) is a comprehensive Python package for genome-wide local ancestry inference in crossbred populations. It integrates PLINK, ADMIXTURE, and LAMP into a streamlined, automated pipeline.

🚀 Features

• Automated Pipeline: End-to-end local ancestry analysis

• Quality Control: Robust filtering and preprocessing with PLINK

• Global Ancestry: Population structure analysis using ADMIXTURE

• Local Ancestry: Fine-scale ancestry segments with LAMP

• Interactive Notebook: Original Colab notebook for exploratory analysis

• Visualization: Comprehensive plots and summary statistics

• Dual Usage: Available as both Python package and Google Colab notebook

📦 Installation

From PyPI

pip install laax

⚙️ Dependencies

LAAX requires these external tools to be installed and available in your system PATH:

• PLINK (v1.9+): For genotype data processing

• ADMIXTURE: For global ancestry estimation

• LAMP: For local ancestry inference

🏁 Quick Start

Basic Usage:

laax --target MyBreed
--ancestors Anc1 Anc2
--input genotypes
--chr-set 30
--output my_results

Advanced Usage:

laax --target MyBreed
--ancestors Anc1 Anc2
--input genotypes
--chr-set 30
--output my_results
--maf 0.05
--hwe 1e-6
--geno 0.1
--mind 0.1

💡 Command Line Usage

laax --target TARGET --ancestors ANCESTOR1 ANCESTOR2 --input INPUT [options]

Required Arguments:

• --target TARGET: Target population name

• --ancestors ANCESTORS ANCESTORS: Two ancestral population names

• --input INPUT: PLINK file prefix (without .bed/.bim/.fam extension)

• --chr-set: Number of chromosomes (default: 26)

Optional Arguments:

• --output OUTPUT: Output directory (default: laax_results)

• --maf MAF: Minor allele frequency threshold (default: 0.05)

• --hwe HWE: HWE threshold (default: 1e-6)

• --geno GENO: SNP missingness threshold (default: 0.1)

• --mind MIND: Individual missingness threshold (default: 0.1)

• --plink-path PLINK_PATH: Path to PLINK executable (auto-detected)

• --admixture-path ADMIXTURE_PATH: Path to ADMIXTURE executable (auto-detected)

• --lamp-path LAMP_PATH: Path to LAMP executable (auto-detected)

📊 Output

The pipeline generates the following outputs in the specified output directory:

• ✅ Quality-controlled genotype data (PLINK format)

• 🌍 Global ancestry proportions (ADMIXTURE Q-files)

• 🧬 Local ancestry segments (LAMP output)

• 📈 Ancestry visualization plots

• 📋 Summary statistics and composition reports

• 🔍 Significant genomic regions

• 📝 Pipeline execution logs and configuration

🛠 Troubleshooting

Common Issues:

• Tool not found: Ensure PLINK, ADMIXTURE, LAMP are in system PATH or specify paths explicitly

• Memory errors: Use smaller datasets or increase system memory

• Installation fails: Try pip install --upgrade laax

• File format errors: Verify PLINK binary format (.bed, .bim, .fam) exists

• Chromosome set mismatch: Adjust --chr-set parameter for your organism

👨‍🔬 About the Author

Dr. Kanaka K. K., PhD, ARS
Scientist
School of Bioinformatics and Computational Biology ICAR-Indian Institute of Agricultural Biotechnology, Ranchi > Be like IIAB!: IIAB is like yogic center where all the sciences (Plant, Animal, Aquatic,Mibrobiology, IT) meet to address emerging issues in food production.

🔎 Spy on me

• Google Scholar
• GitHub: kkokay07
• ResearchGate
• Institute Website