1. Introduction

This is an introductory tutorial for learning genomics mostly on the Linux command-line. Should you need to refresh your knowledge about either Linux or the command-line, have a look here.

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 [KAWECKI2012], [ZEYL2006]. The final aim is to identify the genome variations in evolved lines of E. coli that can explain the observed biological phenotype(s).

1.1. The workflow

The tutorial workflow is summarised in Fig. 1.1.

_images/workflow.png

Fig. 1.1 The tutorial will follow this workflow.

1.2. 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

KAWECKI2012

Kawecki TJ et al. Experimental evolution. Trends in Ecology and Evolution (2012) 27:10

ZEYL2006

Zeyl C. Experimental evolution with yeast. FEMS Yeast Res, 2006, 685–691