This document is the trainee exercise booklet for a 3 day hands-on Next Generation Sequencing workshop developed by Bioplatforms Australia, CSIRO and EMBL-EBI.  This workshop is aimed at bench biologists, PhD students or early career postdoctoral researchers or those new to the analysis of NGS data and assumes no prior knowledge of bioinformatics. This course covers the following topics: data quality control, read alignment, ChIPSeq, RNASeq and de novo assembly. The workshop starts with the Intro to the shell material from Software Carpentry (http://software-carpentry.org/v4/shell/index.html).  Introductory lectures on each topic are presented before trainees move on that topic. The workshop has been delivered a number of times in different cities in Australia to date, in a roadshow style, and is designed to run on virtual machines on the Australian research cloud. Trainees then use NoMachine NX client to provide a remote desktop like connection to their own dedicated VM for the duration of of the workshop.  Various contributors made this workshop possible and they are credited in the introduction to each section.