Course at EMBL-EBI

Metagenomics bioinformatics

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This course will cover the use of publicly available resources to manage, share, analyse and interpret metagenomics data, including marker gene, whole gene shotgun (WGS) and assembly-based approaches. Delegates will gain hands-on experience using a range of data resources and tools, interspersed with lectures. Additionally, there will be the opportunity to discuss the challenges facing researchers in the field.

Who is this course for?

This course is aimed at life scientists who are working in the field of metagenomics, in the early stages of their data analysis, and who may already have some prior experience in using bioinformatics in their research.


Some 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:

  • Submit data to public resources for metagenomics
  • Interpret results and compare with other metagenomics datasets
  • Use a range of tools to perform some data analyses
  • Discuss the pitfalls and challenges in the field
Course content

During this course you will learn about:

  • Data generation: Next Generation Sequencing, amplicon approaches (ribosomal  RNA), whole genome shotgun (WGS) approaches, assembly and metagenome assembled genomes (MAGs)
  • Data analysis: MGnify, HMMER, InterPro, GO, FASTQC, metabolic and pathway analyses
  • Data standards and submission: European Nucleotide Archive (ENA), Genomic Standards Consortium (GSC), SRA, Webin
  • Public resources for metagenomics


Rob Finn
Alex Mitchell
Darren Wilkinson
University of Newcastle, UK
Chris Quince
Warwick Medical School, UK
Lorna Richardson
Josephine Burgin
Sam Holt
Amanda Warr
University of Edinburgh, UK
Alexandre Almeida
Guillermo Rangel


Day 1 – Monday 10th June
11:30 - 12:30 Arrival, registration and lunch  
12:30 - 13:00 An introduction to EMBL-EBI Alexandra Holinski
13:00 - 13:45 Sequencing technologies for metagenomics  Amanda Warr 
13:45 - 14:15 Introduction to metagenomics data analysis: why provenance matters Alex Mitchell
14:15 - 15:00 Limitations of 16S rRNA gene analysis Amanda Warr 
15:00 - 15:30 Break  
15:30 - 17:00 Sequence and metadata submission to ENA (hands on) Josephine Burgin, Sam Holt
17:00 - 17:30 Free time  
17:30 Evening meal Hinxton Hall Restaurant
19:00 Shuttle to Holiday Inn, Duxford   
Day 2 – Tuesday 11th June
08:30 Shuttle to Wellcome Genome Campus   
09:00 - 10:30 Marker genes and taxonomic analysis (hands on) Rob Finn
10:30 - 11:00 Break  
11:00 - 12:00 Estimating sequencing effort Darren Wilkinson
12:00 - 13:00 Lunch  
13:00 - 14:00 Estimating sequencing effort continued (hands on)   Darren Wilkinson
14:00 - 15:00 Functional and taxonomic analysis with MGnify Alex Mitchell
15:00 - 15:30 Break  
15:30 - 17:30 MGnify  and programmatic access (hands on) Alex Mitchell & Rob Finn
17:30 - 18:00 Free time  
18:00 Evening meal Hinxton Hall Restaurant
19:30  Shuttle to Holiday Inn, Duxford   
Day 3 – Wednesday 12th June
08:30  Shuttle to Wellcome Genome Campus  
09:00 - 10:30 Assembly and binning (hands on) Rob Finn
10:30 - 11:00 Break  
11:00 – 12:30 Co-assembly and bin refinement (hands on) Rob Finn
12:30 - 14:00 Lunch and poster session  
14:00 - 15:30 Strain resolution (hands on) Chris Quince
15:30 - 16:00 Break  
16:00 - 17:30 Strain resolution continued (hands on) Chris Quince
17:30 Free time  
18:00 Evening meal Red Lion, Hinxton
20:30  Shuttle to Holiday Inn, Duxford   
Day 4 – Thursday 13th June
08:30 Shuttle to Wellcome Genome Campus  
09:00 - 10:00 Searching the metagenomics peptide database (hands on) Rob Finn & Alex Mitchell
10:00-11:00 Pathways and Systems Lorna Richardson & Alex Mitchell
11:00 - 11:30 Break  
11:30 - 13:00 Viral taxonomic anlaysis in metagenomic data Alex Almeida, Guillermo Rangel
13:00 - 13:15 Course feedback and wrap-up  Alexandra Holinski
13:15 - 14:00 Lunch  
14:15 Shuttle to Cambridge Station  

Please read our page on application advice before starting your application. In order to be considered for a place on this course, you must do the following:

  1. Complete the online application form
  2. Provide a Microsoft Word (.docx) document containing three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words
  3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course

Please submit all documents to Meredith Willmott ( by 12:00 GMT on Friday 22 March, 2019.

Incomplete applications will not be considered.

The course fee includes accommodation and meals.

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This course has ended

10 - 13 June 2019
European Bioinformatics Institute United Kingdom
Meredith Willmott

  • Rob Finn
  • Alex Mitchell
  • Alexandra Holinski

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