Virtual course

Genome-resolved metagenomics bioinformatics

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

This course will cover the use of publicly available resources to manage, share, analyse and interpret metagenomics data, focussing primarily on 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 using containerised tools 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

Vladimir Benes
EMBL
Josephine Burgin
EMBL-EBI
Juan Caballero Perez
EMBL-EBI
Tatiana Gurbich
EMBL-EBI
Maira Ihsan
EMBL-EBI
Varsha Kale
EMBL-EBI
Richard Leggett
Earlham Institute
Sebastien Raguideau
Warwick Medical School, UK
Lorna Richardson
EMBL-EBI
Alexander Rogers
EMBL-EBI
Chris Quince
Earlham Institute

Programme

 

All timing provided in GMT

Time

Subject

Trainer

Day one – Monday 31 October 2022

Introductions, experimental considerations, QC and host decontamination.

09:00 – 09:30

Arrival, check-in, and hangout

Patricia Carvajal López, and Meredith Willmott

09:30 – 09:45

Introduction to virtual training

Patricia Carvajal López

09:45 – 10:15

Participant introductions and networking

All

10:15 – 10:30

Course introduction

Lorna Richardson

10:30 – 10:45

Break

 

10:45 – 12:00

Experimental considerations of metagenomics and Q&A

Vladimir Benes

12:00 – 13:00

Lunch break

 

13:00 – 13:45

QC and decontamination: lecture and Q&A

Varsha Kale

13:45 – 14:45

QC and decontamination: practical and recap

Varsha Kale

14:45 – 15:00

Break

 

15:00 – 15.45

European Nucleotide Archive: lecture and Q&A

Josephine Burgin, and Maira Ihsan

15:45 – 16:30

Flash talks

All

16:30

End of day

 

Day two – Tuesday 1 November 2022

Assembly

09:30 – 09:45

Arrival, check-in, and hangout

Patricia Carvajal López, and Meredith Willmott

09:45 – 10:00

Group activity

All

10:00 – 11:00

Long-read metagenomics: lecture and Q&A

Richard Leggett

11:00 – 11:15

Break

 

11:15 – 12:30

Long-read metagenomics: practical

Richard Leggett

12:30 – 13:30

Lunch break

 

13:30 – 14:30

Tools to assemble short- and long- reads: lecture and Q&A

Juan Caballero

14:30 – 15:00

Assembly and co-assembly: practical

Juan Caballero, and Tanya Gurbich

15:00 – 15:15

Break

 

15:15 – 15:45

Assembly and co-assembly: practical

Juan Caballero, and Tanya Gurbich

15:45 – 16:30

Introduction to MGnifyR

Sandy Rogers

16:30 – 17:00

Flash talks

All

17:00

End of day

 

Day three – Wednesday 2 November 2022

Binning, and MAG generation

09:30 – 09:45

Arrival, check-in, and hangout

Patricia Carvajal López, and Meredith Willmott

09:45 – 10:00

Group activity

All

10:00 – 11:00

Binning and MAG generation: lecture and Q&A

Tanya Gurbich

11:00 – 11:15

Break

 

11:15 – 12:30

Binning and MAG generation: practical

Tanya Gurbich

12:30 – 13:30

Lunch break

 

13:30 – 15:00

Binning and MAG generation: practical

Tanya Gurbich

15:00 – 15:15

Break

 

15:15 – 16:15

ENA Metagenomics Standards and MAG layer: lecture and Q&A

Josephine Burgin, and Maira Ihsan

16:15 – 17:00

Flash talks

All

17:00

End of day

 

Day four – Thursday 3 November 2022

MGnify resources and strain resolution

09:30 – 09:45

Arrival, check-in, and hangout

Patricia Carvajal López, and Meredith Willmott

09:45 – 10:00

Group activity

All

10:00 – 10:30

MGnify MAG resources and API: lecture + Q&A

Sandy Rogers

10:30 – 11:00

MGnify MAG resources and API: practical

Sandy Rogers

11:00 – 11:15

Break

 

11:15 – 12:00

MGnify MAG resources and API: practical

Sandy Rogers

12:00 – 13:00

Break

 

13:00 – 14:00

Strain resolution: lecture + Q&A

Chris Quince

14:00 – 15:00

Strain resolution: practical

Sebastien Raguideau

15:00 – 15:15

Break

 

15:15 – 16:00

Strain resolution: practical

Sebastien Raguideau

16:00 – 16:30

Flash talks

All

16:30

End of day

 

Day five – Friday 4 November 2022

Comparative metagenome analysis

09:30 – 09:45

Arrival, check-in, and hangout

Patricia Carvajal López, and Meredith Willmott

09:45 – 10:45

Comparative metagenome analysis: lecture + Q&A

MGnify team

10:45 – 11:00

Break

 

11:00 – 12:30

Comparative metagenome analysis with MGnifyR: practical

MGnify team

12:30 – 12:45

Final course Q&A

 

12:45 – 13:00

Course wrap-up and feedback

Patricia Carvajal López

13:00

End of course

 

 

Programme may be subject to changes before registration.

Please read our page on application support 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.
  • Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
    • pre-requisite skills and knowledge
    • current work and course expectations
    • data availability
  • 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 midnight on Friday 05 August 2022. Items marked * in the application are mandatory. Incomplete registrations will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Monday 19 August 2022. If you have any questions regarding the application process please contact Meredith Willmott.

Flash talks

All participants will be asked to give a short presentation about their research work as part of the course. These provide an opportunity to share their research with the other participants and provide a forum for discussion. Successful applicants will be required to submit their talks upon registration.

 

 

Applications close
05 August 2022

31 October - 04 November 2022
£200.00
Contact
Meredith Willmott
Open application with selection
30 places

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

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