de novo Assembly 2018

What's the course about?

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 Illumina and Pacbio sequences, including best practices and 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.

What will I learn?

• Understand the strategic setup of a de novo genome sequencing project, combining different types of data in a coherent approach
• Acquire means to define goals for an assembly project and monitor its progress
• Learn to effectively assess the sequencing data sets' quality
• Understand assembly tools' parameters and their effects, being able to progress from a first-pass to a draft sequence release version.