Overview

Learn about the tools, processes, and analysis approaches used by MGnify 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 the assembly-based approaches used in MGnify analysis.

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, or transitioning into 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. If you are not already familiar with this then you must complete this free tutorial before you attend the course:

•  Basic introduction to the Unix environment

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 such as MGnify to identify relevant data for analysis
• Apply relevant tools in the analysis of metagenomic data
• Submit metagenomic data to online repositories for sharing and future analysis
• Apply knowledge in downstream functional and taxonomic 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 including MGnify, InterPro, GO, FASTQC, and pathway analyses
• Data standards and submission:
  • European Nucleotide Archive (ENA)
  • Genomic Standards Consortium (GSC)
  • Webin
• MGnify metagenomic data analysis workflows

Trainers

Please read our support page 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 23:59 BST on 25 June 2023. 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 17 July 2023. If you have any questions regarding the application process please contact Shereen Pethania.

The registration fee includes:

• Catering as detailed on the course programme
• Accommodation for four nights (9, 10, 11, and 12 October)
• Bespoke course handbook with links to all course materials
• Use of a computer in the EMBL-EBI training suite throughout the course
• Shuttle bus on the final course day to Cambridge train station

Accommodation 

Hotel rooms will be provided onsite at Hinxton Hall Conference Centre. Please contact them directly if you wish to arrange to stay additional nights around the course dates.

Catering

The course includes catering as detailed on the programme tab. Successful applicants will be asked for any dietary requirements and allergies upon registration. 

Course materials

The course materials from the 2022 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 2023 edition.

Flash talks

All participants will be asked to give a short presentation about the services they provide as core facility managers and/or their research work as part of the course. These talks provide an opportunity to share their research with the other participants and provide a forum for discussion. Further details will be provided following registration.

COVID-related information

Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing.

Please also note that there are delays in the issuing of visas from the UK Government. We encourage you to check if you need a visa and apply in plenty of time before travelling. Current waiting times are more than four weeks. For more information please visit the UK Government website.