• Event
  • Scientific training

De Novo Assembly 2019

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. The course will consist of a mixture of conceptual lectures, methodological lectures and hands on sessions, as well as group activities and discussions.

Start date:

11 February 2019

End date:

14 February 2019

Time:

09h30 - 17h00

Venue:

Earlham Institute

Registration deadline:

23 December 2018

Cost:

£300

About the event.

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.

Programme.

Day 1 - 11 February 2019

Time

Topic

09:30 - 17:00

*Programme subject to change, although start and finish times remain as stated*

09:30 - 10:00

Registration

10:00 - 10:15

Welcome and getting connected

10:15 - 11:15

Course introduction & short talks by participants

11:15 - 12:30

Why are we here?

12:30 - 13:30

Lunch

13:30 - 14:30

Sequencing technologies overview

14:30 - 15:00

Genome assembly introduction

15:00 - 15:30

Coffee break

15:30 - 17:00

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

Day 2 - 12 February 2019

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 (cont'd)

14:30 - 15:00

Coffee break

15:00 - 17:00

Data QC concepts

17:00 - 17:30

Overview of example datasets

19:30 - 22:00

Course dinner - Venue: Trattoria Rustica

Day 3 - 13 February 2019

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

First pass assembly and QC concepts + hands-on

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

Day 4 - 14 February 2019

Time

Topic

09:00 - 09:30

Morning coffee

09:30 - 11:00

Assembly pipelines: hands-on

11:00 - 11:30

Coffee break

11:30 - 13:00

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

13:00 - 13:15

Feedback

13:15 - 14:00

Lunch

14:00 - 16:00

(Optional) Trainers will be available for Q&A session

Fees and accommodation.

Registration includes lunch, refreshments, access to the training materials, plus course dinner (venue to be confirmed)