What is the workshop 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 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.
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.
- Learn how basic algorithmic parameters affect assemblies.
- Understand assembly tools' parameters and their effects, being able to progress from a first-pass to a draft sequence release version.
- Review existent QC metrics for assembly projects and their significance.
Prerequisites:
Familiarity with linux is essential to ensure participants are able to go through hands on and concentrate on the actual course topics rather than having to pass the hurdles of basic command line.
Participants will be required to follow a pre-course tutorial on linux.
Useful background reading on background concepts to Next Generation Sequencing technologies can be found here.
Essential pre-reading for this course provides an introduction to k-mers. Familiarity with the concepts and language will ensure we can cover greater depth in this course.
Target audience:
This course is aimed at post-doctoral researchers and advanced PhD students who are already involved or embarking in de novo sequencing projects.
