Population Genomics Workshop

Workshop delivered by Sean Harrington & Vikram Chhatre

Table of Contents

1. High Performance Computing

• Week 1: Working with Teton computing Environment

2. iPyRAD Pipeline to Process Sequence Data

• Week 1: Nextgen Sequencing Data Quality Control

3. Manual Quality Control of Sequence Data

• Week 2: FASTQ Format

• Week 2: Demultiplexing Samples

• Week 2: Quality assessment and trimming

4. Read Mapping and Variant Calling

• Week 3: Read Mapping

• Week 3: Variant Calling

• Week 3: Variant Call Format (VCF)

5. Population structure and inference of selection

• Week 3: Overview of structure and selection

• Week 4: Admixture Analysis

• Week 4: DAPC & snmf Analysis

• Week 5: Selection Analysis with Bayescan

6. Make Your Work Reproducible and Publicly Available

• Week 5: A Git Repo for your Publication