This lessons are part of a two weeks course directed at MSc and phD students following a non-bioinformatics curriculum. It aims to introduce students to the command line in order to use tools to analyse whole genome sequence data and showcases analyses methods such as SNP calling, pangenome analysis and clustering methods that have been introduced during the lectures. This computer practical uses data from this publication.

This lessons are partially based on the Data Carpentry Genomics lesson and are styled with the Software Carpentry lesson template which are made available under the (Creative Commons Attribution license](https://creativecommons.org/licenses/by/4.0/)