Course Modules
Getting Started
Lab 0.1: Environment Setup
Setting up your computational environment for genetic analysis
Lab 0.2: Getting Data
Overview of data resources for genetic analysis
Lab 0.3: OpenSNP Data
Obtaining and processing OpenSNP genetic data
Lab 0.4: 1000 Genomes Data
Accessing and working with 1000 Genomes Project data
Data Exploration & Preparation
Lab 1: Exploring Data
Understanding population genomic data structure
Lab 2: Processing Raw DNA
Converting and preparing DNA profile data
Lab 3: Quality Control
Ensuring data quality for genetic analysis
IBD Detection
Lab 4: IBIS
Identity-by-descent detection using IBIS
Lab 5: Hap-IBD
IBD detection with haplotype-based methods
Lab 6: Refined-IBD
Advanced techniques for IBD segment detection
Simulation & Evaluation
Lab 7: Ped-Sim
Simulating genetic data from known pedigrees
Lab 8: IBD Evaluation
Evaluating IBD detection methods
Lab 9: MSPrime
Coalescent-based genetic simulation
Pedigree Reconstruction
Lab 10: Distributions
Statistical analysis of genetic relatedness
Lab 11: Bonsai Introduction
Reconstructing pedigrees from genetic data
Advanced Bonsai Specialization
Lab 12: Bonsai Fundamentals
Fundamentals of genetic genealogy and IBD segments
Lab 13: Mathematical Foundations
Mathematical principles behind Bonsai algorithm
Lab 14: Data Structures
Data structures and algorithmic design in Bonsai
Lab 15: Model Calibration
Calibrating Bonsai models for optimal performance
Lab 16: Architecture
Architecture and implementation of Bonsai
Lab 17: Likelihood Calculations
Advanced likelihood calculations in Bonsai
Lab 18: Data Quality
Handling data quality issues in pedigree reconstruction
Lab 19: Advanced Construction
Advanced pedigree construction techniques
Lab 20: Visualization
Visualizing and interpreting pedigree structures
Lab 21: Applications
Real-world applications of Bonsai
Additional Resources
Learning Pathway
This course is structured as a progressive learning journey:
Environment Setup
Lab 0.1
Data Acquisition
Labs 0.2-0.4
Data Exploration
Lab 1
Data Processing
Lab 2
Quality Control
Lab 3
IBD Detection
Labs 4-6
Simulation
Labs 7-9
Statistics
Lab 10
Bonsai Algorithm
Labs 11-21
Course Structure: This course builds progressively from foundational skills to advanced topics. Begin with environment setup and data acquisition, then move through data processing and quality control. The middle section covers IBD detection and simulation techniques. The final section explores the Bonsai algorithm for pedigree reconstruction in depth, with specialized labs covering its mathematical foundations, architecture, and applications.