• Event
  • Scientific training

De Novo Assembly 2020

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:

09 March 2020

End date:

13 March 2020

Time:

09h30 - 17h00

Venue:

Earlham Institute

Registration deadline:

19 January 2020

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 and assembly improvement.

Practical exercises will be performed on small-scale real and simulated datasets. 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 and assembly graphs.

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 input data, algorithms and paramaters affect assembly results
  • Learn how to progress from a first-pass to a draft sequence release version
  • Review existent QC metrics for assembly projects and their significance
  • Graph based approaches for assembly

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. Participants will also be required to follow a pre-course tutorial on Linux.

Participants also need to have a working, basic understanding of Python. Participants should complete the Software Carpentry lesson titled 'Programming with Python',

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 - 09 March 2020

Time

Topic

09:30 - 10:00

Registration

10:00 - 10:30

Welcome and Introduction

10:30 - 11:30

Short talks by participants

11:30 - 12:00

Why are we here?

12:00 - 12:30

Lunch

13:00 - 14:00

Sequencing technologies overview

14:00 - 15:00

Genome assembly introduction

15:00 - 15:30

Coffee break

15:30 - 16:00

Push-a-button assembly

16:00 - 17:00

Assembly graphs

Day 2 - 10 March 2020

Time

Topic

09:00 - 09:30

Morning coffee

09:30 - 11:00

K-mer counting and K-mer spectra

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

Pin the K-mer spectra

14:30 - 15:00

Coffee break

15:00 - 15:45

Checking and improving assemblies

17:00 - 17:30

Hands-on: Checking and improving assemblies

19:00 - 21:00

Course dinner

Day 3 - 11 March 2020

Time

Topic

09:00 - 09:30

Morning coffee

09:30 - 10:30

First pass assembly and data QC

10:30 - 11:00

Coffee break

11:00 - 12:30

Hands-on: First pass assembly and QC concepts

12:30 - 13:30

Lunch

13:30 - 14:30

Short and long reads: Content first vs Structure first assembly

14:30 - 15:00

Hands-on: Long read assembly

15:00 - 15:30

Coffee break

15:30 - 16:30

Longer-range data: Concepts and tools

16:30 - 17:30

Lecture/Hands-on: hybrid assembly

Day 4 - 12 March 2020

Time

Topic

09:00 - 09:30

Morning Coffee

09:30 - 10:30

Real life assembly pipelines

10:30 - 11:00

Coffee break

11:00 - 13:00

Final Hands-on session

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)

  • Register today.

Registration deadline: 19 Jan 2020 - 00:00

Participation: Open application with selection process