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 delivered content will involve participants learning via live lectures and 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 training infrastructure.

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:

• Introduction to the Unix environment – https://swcarpentry.github.io/shell-novice/index.html 
• Introduction to R – https://swcarpentry.github.io/r-novice-inflammation/ 

What will I learn?

Learning outcomes

After the 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:
  • European Nucleotide Archive (ENA)
  • Genomic Standards Consortium (GSC)
  • SRA
  • Webin
• Metagenomic data analysis workflows

Trainers

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 one 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 Sunday 9 June 2024. 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 24 June 2024. If you have any questions regarding the application process please contact Meredith Willmott.

The registration fee of £100.00 includes:

• access to the full five-day course programme
• access to a bespoke online course handbook
• secure community space on Slack
• virtual machine to work on that is accessed via the internet
• dedicated online support team
• course certificate on completion of the course

Course materials

The course materials from the 2023 edition of the course are now live and available for you to use. They provide a mixture of pre-recorded lectures, presentations, and practicals from the course, and will give you a snapshot of what to expect in the 2024 edition.

Posters

All participants are expected to present a poster that will be displayed virtually during the course. Successful applicants will be asked to submit their poster upon registration. 

All posters should:

•          PDF format
•          be in a portrait orientation
•          include your photograph and contact information

We expect the posters to act as a talking point between you, other participants, and the trainers on the course. The posters will be available during the week. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants.

Financial assistance 

Limited financial assistance is provided by EMBL-EBI Training in the form of registration fee waivers. 
Your place in the course is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver
The fee waiver will cover the registration fee that you have paid to attend the course.

Application
You may apply for financial assistance when submitting your application. In your application, you will be asked to provide justification for the financial assistance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your course application.

Selection
The scientific organisers will select the recipients of financial assistance during the course application selection process. Results will be communicated along with the course application outcome. Selection results do not impact your acceptance to the course. Selection for registration fee waivers is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career with priority given to applicants from low and middle-income countries.