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:
- Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix
- Basic R concept tutorials: www.r-tutor.com/r-introduction
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:
- Different types of metagenomic data (short-read and long-read)
- Assembly and metagenome assembled genomes (MAGs)
- Data analysis: MGnify, HMMER, InterPro, GO, FASTQC, and pathway analyses
- Data standards and submission:
- Metagenomic data analysis workflows
Trainers
Vladimir Benes
EMBL Josephine Burgin
EMBL-EBI Juan Caballero Perez
EMBL-EBI Grisel Alejandra Escobar Zepeda
EMBL-EBI Tatiana Gurbich
EMBL-EBI Maira Ihsan
EMBL-EBI Varsha Kale
EMBL-EBI Jennifer Lu
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 Shereen Pethania
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
Maira Ihsan, and Josephine Burgin
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 Shereen Pethania
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 Viral Annotations: practical
Varsha Kale
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 Shereen Pethania
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
Maira Ihsan, and Josephine Burgin
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 Shereen Pethania
09:45 – 10:00
Group activity
All
10:00 – 10:30
MGnify MAG resources: lecture + Q&A
Sandy Rogers
10:30 – 11:00
Programmatic access to MGnify resources with APIs and notebooks: practical
Sandy Rogers
11:00 – 11:15
Break
11:15 – 12:00
Programmatic access to MGnify resources with APIs and notebooks: 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 Shereen Pethania
09:45 – 10:45
Comparative metagenome analysis: lecture + Q&A
Jen Lu, and Ales Escobar
10:45 – 11:00
Break
11:00 – 12:30
Comparative metagenome analysis with MGnifyR: practical
Jen Lu, and Ales Escobar
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.
EMBL
EMBL-EBI
EMBL-EBI
EMBL-EBI
EMBL-EBI
EMBL-EBI
EMBL-EBI
EMBL-EBI
Earlham Institute
Warwick Medical School, UK
EMBL-EBI
EMBL-EBI
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 Shereen Pethania |
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 |
Maira Ihsan, and Josephine Burgin |
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 Shereen Pethania |
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 Viral Annotations: practical |
Varsha Kale |
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 Shereen Pethania |
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 |
Maira Ihsan, and Josephine Burgin |
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 Shereen Pethania |
09:45 – 10:00 |
Group activity |
All |
10:00 – 10:30 |
MGnify MAG resources: lecture + Q&A |
Sandy Rogers |
10:30 – 11:00 |
Programmatic access to MGnify resources with APIs and notebooks: practical |
Sandy Rogers |
11:00 – 11:15 |
Break |
|
11:15 – 12:00 |
Programmatic access to MGnify resources with APIs and notebooks: 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 Shereen Pethania |
09:45 – 10:45 |
Comparative metagenome analysis: lecture + Q&A |
Jen Lu, and Ales Escobar |
10:45 – 11:00 |
Break |
|
11:00 – 12:30 |
Comparative metagenome analysis with MGnifyR: practical |
Jen Lu, and Ales Escobar |
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.