Genomics Tutorial

This is an introductory tutorial for learning computational genomics mostly on the Linux command-line. You will learn how to analyse next-generation sequencing (NGS) data. The data you will be using is real research data. The final aim is to identify genome variations in evolved lines of bacteria that can explain the observed biological phenotypes.

This tutorial have been adapted from a tutorial created by Sebastian Schmeier who presented it in the Massey University course Genome Science. The original tutorial can be accessed here: https://genomics.sschmeier.com/. Note that the original tutorial is licensed under the MIT license and the source code to the original tutorial can be accessed on github.

The overall work-flow for the tutorial is as follows:

tutorial workflow

Contents

  1. Introduction
  2. Preparation
  3. Quality Control
  4. Genome Assembly
  5. Read Mapping
  6. Taxonomic Investigation
  7. Variant Calling
  8. Genome Annotation