Virtual course

Metagenomics bioinformatics

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Learn about the tools, processes and analysis approaches used in the field of metagenomics.

This course will cover the use of publicly available resources to manage, share, analyse and interpret metagenomics data; including marker gene, whole gene shotgun (WGS) and assembly-based approaches.

The virtually-delivered content will involve participants learning via pre-recorded lectures and live presentations, followed by live Q&As with the trainers. Practical experience will be developed in group activities and in computational exercises run in Docker containers on our virtual training infrastructure.

Participants will need to be available between the hours of 09:00-17:00 GMT each day of the course.

Who is this course for?

This course is aimed at life scientists who are working in the field of metagenomics and are currently in the early stages of data analysis. Participants should have some prior experience of using bioinformatics in their research.

The practical sessions in the course require a basic understanding of the Unix command line and the R statistics package. If you are not already familiar with these then please ensure that you complete these free tutorials before you attend the course:

What will I learn?

Learning outcomes

After this course you should be able to:

  • Conduct appropriate quality control and decontamination of metagenomic data and run simple assembly pipelines on short read data
  • Utilise public datasets and resources to identify relevant data for analysis
  • Apply relevant tools in the analysis of metagenomic data
  • Submit metagenomics data to online repositories for sharing and future analysis
  • Apply knowledge in the areas of strain resolution and additional functional analysis
Course content

During this course you will learn about:

Trainers

Robb Finn
EMBL-EBI, UK
Lorna Richarson
EMBL-EBI, UK
Varsha Kale
EMBL-EBI, UK
Martin Beracochea
EMBL-EBI, UK
Chris Quince
Warwick Medical School, UK
Sebastien Raguideau
Warwick Medical School, UK
Georg Zeller
EMBL Heidelberg
Jakob Wirbel
EMBL Heidelberg
Josephine Burgin
EMBL-EBI, UK
Sam Holt
EMBL-EBI

Programme

 

Time

Subject

Trainer

Day 1 – Monday 8 November

Introductions, QC & host decontamination, assembly

09:00-09:30

Arrival, check-in and hangout

Patricia Carvajal López & Marina Pujol

09:45-10:00

Introduction to virtual training

Patricia Carvajal López

10:00-10:30

Participant introductions and networking

All

10:30-10:45

Break

 

10:45-11:15

Course introduction

Rob Finn

11:15-12:00

Quality control and host-decontamination - lecture + Q&A

Varsha Kale

12:00-12:45

QC & decontamination - practical

Varsha Kale

12:45-13:00

QC & decontamination - practical recap

Varsha Kale

13:00-14:00

Break

 

14:00-15:00

European Nucleotide Archive – lecture + Q&A

Josephine Burgin & Sam Holt

15:00-15:15

Break

 

15:15-16:30

Tools to assemble short reads – lecture + Q&A

Rob Finn

16:30-17:00

Flash talks

All

17:00

End of day

 

Day 2 – Tuesday 9 November

Functional analysis & MGnify services

09:30-09:45

Arrival, check-in and hangout

Patricia Carvajal López & Marina Pujol

09:45-10:00

Group activity

All

10:00-11:00

MGnify services – lecture + Q&A

Lorna Richardson

11:00-11:15

Break

 

11:15-12:15

MGnify services – practical

Lorna Richardson

12:15-12:30

MGnify services – practical recap

Lorna Richardson

12:30-13:30

Break

 

13:30-14:30

MGnify and R - lecture + Q&A

MGnify Team

14:30-15:30

MGnify and R - practical

MGnify Team

15:30-15:45

Break

 

15:45-16:00

MGnify and R - Practical recap

MGnify Team

16:00-16:30

Flash talks

All

16:30

End of day

 

Day 3 – Wednesday 10 November

Assembly binning, MAGs and submission to ENA

09:30-09:45

Arrival, check-in and hangout

Patricia Carvajal López & Marina Pujol

09:45-10:00

Group activity

All

10:00-11:00

Assembly, binning and MAG generation – lecture + Q&A

MGnify Team

11:00-11:15

Break

 

11:15-12:30

Assembly, binning and MAG generation – practical

MGnify Team

12:30-13:30

Break

 

13:30-15:00

Assembly, binning and MAG generation – practical

MGnify Team

15:00-15:15

Assembly, binning and MAG generation – practical recap

MGnify Team

15:15-15:30

Break

 

15:30-16:30

ENA Metagenomics Standards – lecture + Q&A

Josephine Burgin and Sam Holt

16:30-17:00

Flash talks

All

17:00

End of day

 

Day 4 – Thursday 11 November

MGnify resources and strain resolution

09:30-09:45

Arrival, check-in and hangout

Patricia Carvajal López & Marina Pujol

09:45-10:00

Group activity

All

10:00-11:00

MGnify MAG resources – lecture + Q&A

Martin Beracochea

11:00-11:15

Break

 

11:15-12:15

MGnify API data hunt - practical

Martin Beracochea

12:15-12:30

MGnify API data hunt - practical recap

Martin Beracochea

12:30-13:30

Break

 

13:30-14:30

Strain resolution - lecture

Chris Quince

14:30-15:30

Strain resolution - practical

Sebastien Raguideau

15:30:15:45

Break

 

15:45-16:15

Strain resolution - practical

Sebastien Raguideau

16:15-16:30

Strain resolution - practical recap

Sebastien Raguideau

16:30-17:00

Flash talks

All

17:00

End of day

 

Day 5 – Friday 12 November

Comparative metagenome analysis

09:30-09:45

Arrival, check-in and hangout

Patricia Carvajal López & Marina Pujol

09:45-10:45

Comparative metagenome analysis – lecture + Q&A

Georg Zeller

10:45-11:00

Break

 

11:00-13:00

Comparative metagenome analysis – practical +Q&A

Jakob Wirbel & Georg Zeller

13:00-13:15

Final course Q&A

 

13:15-13:30

Course wrap-up and feedback

Patricia Carvajal López

13:30

End of course

 

Please read our page on application advice before starting your application. In order to be considered for a place on this course, you must do the following:

  • Complete the online application form providing answers as directed
  • Ensure you add relevant information to the "Application submission" section where you are asked to provide three 100-word paragraphs that cover your:
    • scientific biography/work experience
    • current research interests
  • Upload a letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course

Please submit all documents during the application process by 23:59 GMT, Friday 3rd September.

Incomplete applications will not be considered.

All applicants will be informed of the status of their application (successful, waiting list, rejected) by Friday 27 September.

Participant flash talks

There will be an opportunity for all participants to give a short presentation as part of the course covering their work. These will offer a chance to share research with the other participants and an opportunity for them and trainers to ask questions. Further details will be provided following registration.

Apply now
Applications close
03 September 2021

08 - 12 November 2021
£200
Contact
Marina Pujol
Open application with selection
30 places

Organisers
  • Patricia Carvajal Lopez
    EMBL-EBI
  • Rob Finn
    EMBL-EBI
  • Lorna Richardson
    EMBL-EBI

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