• Event
  • Scientific training

de novo Assembly 2017

The course will provide a hands-on introduction to de novo assembly, followed by in-depth analysis of the key stages in the process.

Start date:

14 March 2017

End date:

17 March 2017

Time:

09h30 - 16h00

Venue:

Earlham Institute

Registration deadline:

10 March 2017

Cost:

£200.00

About the event.

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.

Programme.

Day 1 - 14 March 2017

Time

Topic

09:30 - 10:00

Registration

10:00 - 10:30

Welcome and connecting to NoMachine

10:30 - 11:30

Course introduction and short talks by participants

11:30 - 13:00

Why are we here

13:00 - 14:00

Lunch

14:00 - 15:30

Sequencing technologies overview

15:30 - 16:00

Coffee break

16:00 - 17:00

Genome assembly introduction and hands on: a simple example (data and workflow overview)

17:00 - 18:30

Pizza and beer

Day 2 - 15 March 2017

Time

Topic

09:00 - 09:30

Morning coffee

09:30 - 11:00

Genome assembly introduction and hands on: a simple example (assembly and review)

11:00 - 11:30

Coffee break

11:30 - 12:30

Genome assembly and validation: Concepts and tools

12:30 - 13:30

Lunch

13:30 - 14:30

Genome assembly and validation: Concepts and tools

14:30 - 15:00

Coffee break

15:00 - 17:00

Data QC concepts

17:00 - 17:30

Overview of example datasets

Day 3 - 16 March 2017

Time

Topic

09:00 - 09:30

Morning coffee

09:30 - 10:30

Hands on: data QC

10:30 - 11:00

Coffee break

11:00 - 13:00

Hands on look at first pass assembly and QC concepts

13:00 - 14:00

Lunch

14:00 - 15:30

Assembly improvements, scaffolding and gap closing: Concepts and tools

15:30 - 16:00

Coffee break

16:00 - 17:30

Real life assembly pipelines

19:30 - 21:00

Course dinner (Italian)

Day 4 - 17 March 2017

Time

Topic

09:00 - 09:30

Morning coffee

09:30 - 11:00

Hands on with assembly pipelines

11:00 - 11:30

Coffee break

11:30 - 13:00

Assembly pipelines: Further assembly validation and longer-range data incorporation concepts

13:00 - 14:00

Lunch

14:00 - 16:00

Q&A - closing remarks and feedback (expect people to bring their problems for this session)

Further information.

Course 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.

Target audience

This course is aimed at advanced PhD students and post-doctoral researchers who are already involved or embarking in de novo sequencing projects.

Fees and accommodation.

Registration costs £200.00, which is inclusive of lunch and refreshments, course dinner and course materials.

Related reading.