- 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:
Enquiries:
training@earlham.ac.uk
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, then proceed to look at experimental approaches and emerging technologies. 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 - 10:00
Practical considerations for library preparation and sequencing of metagenomes - Karim Gharbi
10:00 - 11:00
Lecture:
Current pipelines for processing amplicon sequences - Falk Hildebrand
11:00 - 11:30
Coffee
11:30 - 13:00
Hands-on session:
bioinformatic processing amplicon sequences with LotuS pipeline - Falk Hildebrand
13:00 - 14:00
Lunch
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
Coffee
10:30 - 12:30
Hands-on session:
Generating a MEGAN file and using MEGAN to produce publication-ready figures - Ryan Joynson
12:30 - 13:30
Lunch
13:30 - 15:30
Lecture and hands-on session:
Assembly of metagenomic samples - Martin Ayling
15:30 - 16:00
Coffee
16:00 - 17:00
Tutorial:
CyVerse UK virtual machines - Alice Minotto
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