The course will provide an introduction to de novo assembly, with a hands on introduction followed by in-depth analysis of the key steps in the process. It covers several aspects such as the initial setup of a de novo genome sequencing project, quality control and preprocessing of datasets, generation and evaluation of first pass assemblies, assembly improvement and finishing.

Practical exercises will be performed on small-scale real datasets, including short and long reads. We will present best practices and provide tips based on EI's faculty experience.

The course will consist of a mixture of conceptual lectures, methodological lectures and hands on sessions, as well as group activities and discussions. The participants will gain first-hand experience and understanding on NGS assembly, working with the assistance of the faculty, troubleshooting small problems, and reviewing the results.

This year, we will be including more in-depth content on working with mixed datasets comprising different sequencing technologies, plus hands sessions covering basic assembly algorithm parameterisation.