• Event
  • Scientific training

Metagenomics: Data Analysis and Interpretation

This course will provide an overview of the main aspects involved in metagenomics data analysis and discussion around the interpretation and actual examples of the impact and applications of metagenomics derived research.

Start date:

16 September 2019

End date:

19 September 2019

Time:

09h00 - 17h00

Venue:

Earlham Institute

Organiser:

Registration deadline:

16 June 2019

Cost:

£400

About the event.

This course will provide an overview of the main aspects involved in metagenomics data analysis and discussion around the interpretation and actual examples of the impact and applications of metagenomics derived research. A substantial part of the course will be devoted to hands-on experience with bioinformatics resources and tools relevant in metagenomics data analysis.

Participants will start with an overview of NGS technologies, a look at experimental approaches and emerging technologies, including a tour of Earlham Institute’s Genomic Pipelines laboratories. Then the remainder of the course will be spent in front of the computers learning how to produce metagenomic assemblies, and taking participants from data to publication-ready figures.

What will I learn?

  • An overview of NGS for metagenomics including current projects and emerging technologies
  • A practical understanding of the instrumentation and methods used to generate and sequence metagenomics libraries
  • An overview of software for analysis and interpretation of metagenomics datasets and some basic analytical workflows
  • Hands-on experience of a case study dataset including FastQC, trimming and host removal
  • Understanding assembly principles and the latest metagenomics assembly tools
  • Hands on experience in metagenomics assembly
  • Using MEGAN to explore metagenomic including taxonomic and functional annotation, multiple comparison methods and production of publication quality images
  • An overview and hands on experience in public data resources for metagenomics e.g. IMG/M, EBI Metagenomics, MG-RAS

Course prerequisites

You are expected to be familiar and competent with a range of laboratory equipment and follow GLP.

Some basic knowledge and experience in LINUX is desirable. If no previous experience, it is recommended that you follow a tutorial such as the one here prior to attending the course.

Target audience

This course is aimed at advanced PhD students and post-doctoral researchers who are currently undertaking, or are in the planning stages of, a metagenomics project.

Programme.

Day 1 - 16 September 2019

Time

Topic

00:00 - 00:00

**Please note that this programme is tentative and may be subject to change**

10:00 - 11:00

Registration and Coffee

11:00 - 11:15

Welcome and Introduction

11:15 - 12:30

Flash presentations from Delegates

12:30 - 13:30

Lunch

13:30 - 14:30

Lecture:
Overview of NGS technologies - Karim Gharbi

14:30 - 15:00

Coffee

15:00 - 16:00

Keynote Lecture:
Lindsay Hall, QIB

16:00 - 17:00

Lecture:
Metagenomics Approaches - Prof. Neil Hall

19:30 - 22:00

Dinner - Venue TBC

Day 2 - 17 September 2019

Time

Topic

08:30 - 09:00

Morning Coffee

09:00 - 10:30

Tour of EI’s Genomic Pipelines Labs - Karim Gharbi

10:30 - 11:00

Coffee

11:00 - 12:00

Practical considerations for library preparation and sequencing of metagenomes - Karim Gharbi

12:00 - 13:00

Lunch

13:00 - 14:00

Emerging Technologies & Case Studies:
Nanopore (Richard Leggett)
Single Cell (Iain Macaulay)
Case Study (Mark McMullan, TBC)

14:00 - 15:00

Lecture:
Introduction to tools and approaches for analysing and interpreting metagenomic datasets - Richard Leggett

15:00 - 15:30

Coffee

15:30 - 17:00

Lecture and hands-on session:
Next Generation Sequencing data analysis for metagenomics - Richard Leggett

Day 3 - 18 September 2019

Time

Topic

08:30 - 09:00

Morning Coffee

09:00 - 10:00

Introduction to MEGAN - Ryan Joynson

10:00 - 10:30

Hands-on session:
Generating a MEGAN file - Ryan Joynson

10:30 - 11:00

Coffee

11:00 - 13:00

Hands-on session:
Using MEGAN to produce publication-ready figures - Ryan Joynson

13:00 - 14:00

Lunch

14:00 - 15:00

Lecture:
Assembly of metagenomic samples - Martin Ayling

15:00 - 15:30

Coffee

15:30 - 17:00

Hands-on session:
Assembly of metagenomic samples - Martin Ayling

Day 4 - 19 September 2019

Time

Topic

08:30 - 09:00

Morning coffee

09:00 - 10:30

Lecture:
Meta-analysis across multiple metagenomic projects and identifying novel organisms - Alex Mitchell

10:30 - 11:00

Coffee

11:00 - 12:00

Lecture:
Functional and taxonomic analysis with MGnify: extracting knowledge from microbiome data - Alex Mitchell

12:00 - 13:00

Lunch

13:00 - 14:00

Hands-on:
Functional and taxonomic analysis with MGnify: extracting knowledge from microbiome data - Alex Mitchell

14:00 - 15:00

Final Q&A, feedback, coffee and depart

Further information.

Registration includes lunch and refreshments, plus access to training materials and the course dinner

Course dinner: Venue TBC

  • Register today.

Registration deadline: 16 June 2019

Participation: Open application with selection process