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.
Additional information
This course is currently under construction and so details are subject to change.
We plan to deliver this course in an in-person manner onsite at our training suite at EMBL-EBI, Hinxton. Hybrid options are not currently available. We reserve the right to change the format of this course or cancel it, due to the ongoing coronavirus pandemic.
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.
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?
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
Applications close: 25 June 2023
Course dates: 9 - 13 October 2023
Course fee: £750.00 (inclusive of four nights accommodation and catering)