Genomics Workshop

This hands-on workshop is designed to introduce students to the basic analysis pipeline for Next-Generation Sequencing (NGS) reads, specifically from the Illumina platform for population genetics analysis.

We’ll focus on whole genome resequencing data (WGS), though the same pipeline may also be applied to RAD-seq or amplicon-seq data (with minor modifications) if a reference genome is available.

By the end of the workshop, participants will understand how to:

• Work with raw sequencing data (FASTQ files)
• Perform quality control and preprocessing
• Map reads to a reference genome
• Call and filter genetic variants (SNPs/indels)

Pre-requisites & Setup

Before joining the workshop, please make sure you can access a Unix/Linux shell environment, as all commands and tools will be run from the command line.

Windows users may install MobaXterm. Mac/Linux systems already have a terminal available.

• Basic knowledge of Linux commands: Understanding Linux Commands

Recommended Resources

How Illumina Sequencing works?

Watch this video to understand the technology

Linux Shell Basics

• Basic Tutorial
• Linux Basics Solutions

Advanced Linux Commands

• Advanced Tutorial
• Linux Advance Solutions

Dataset Download Instructions

Download Here

1. Go to the link above.
2. Create a directory: mkdir name_of_directory
3. Use wget to download files.

Workshop Pipeline

1. Initial Processing of FASTQ Files

• Script: FASTQ File Processing
• Solutions File: FASTQ File Processing Solutions

2. Mapping Reads to Reference Genome

• Script: Read Mapping and Sorting
• Solutions File: Read Mapping and Sorting Solutions

3. Identifying Variants (SNPs/Indels)

Script:

4. Filtering Variants

• Script: Variant Filtering
• Solutions File: Variant Filtering Solution

5. Population Structure & Visualization

Script:

© Content adapted from PoODL-CES Genomics_learning_Workshop.