Genomics Tutorial - Introduction

This is an introductory tutorial for learning genomics mostly on the Linux command-line. Should you need to refresh your knowledge about the Linux Terminal, see Linux 101.

In this tutorial you will learn how to analyse next-generation sequencing (NGS) data. The data you will be using is actual research data. The experiment follows a similar strategy as in what is called an "experimental evolution" experiment (1,2). The final aim is to identify the genome variations in evolved lines of E. coli that can explain the observed biological phenotype(s).

The work-flow

The tutorial work-flow is summarised as follows: tutorial workflow

Learning outcomes

During this tutorial you will learn to:

  • Check the data quality of an NGS experiment
  • Create a genome assembly of the ancestor based on NGS data
  • Map NGS reads of evolved lines to the created ancestral reference genome
  • Call genome variations/mutations in the evolved lines
  • Annotate a newly derived reference genome
  • Find variants of interest that may be responsible for the observed evolved phenotype(s)

References

  1. Kawecki, T. J., Lenski, R. E., Ebert, D., Hollis, B., Olivieri, I., & Whitlock, M. C. (2012). Experimental evolution. Trends in ecology & evolution, 27(10), 547-560.

  2. Zeyl, C. (2006). Experimental evolution with yeast. FEMS yeast research, 6(5), 685-691.