de novo Assembly 2017

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.