16/07/2018 - 20/07/2018

European Bioinformatics Institute (EMBL-EBI) – Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD
-, United Kingdom

Metagenomics Bioinformatics 2018

Code: 2018-metagen
Price: free
Location: European Bioinformatics Institute (EMBL-EBI) – Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD



European Bioinformatics Institute (EMBL-EBI) – Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom


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.

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.

Further details on the program are provided here.

 Complete trainer list:

  • Clara Amid – EMBL-EBI, UK
  • Rob Finn – EMBL-EBI, UK
  • Alexandra Holinski – EMBL-EBI, UK
  • Alex Mitchell – EMBL-EBI, UK
  • Chris Quince – Warwick Medical School
  • Jeena Rajan – EMBL-EBI, UK
  • Joao Matias Rodrigues – University of Zurich
  • Aleksandra Ola Tarkowska – EMBL-EBI, UK
  • Darren Wilkinson – University of Newcastle, UK
  • Georg Zeller – EMBL Heidelberg

Learning goals:

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


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:

Basic introduction to the Unix environment:

Basic R concept tutorials:


metagenomics, bioinformatics, data analysis, course, training


  • Data generation: Next Generation Sequencing, amplicon-based approaches (ribosomal  RNA), WGS, assembly
  • Data analysis: The EBI Metagenomics Portal, HMMER, InterPro, GO, FASTQC, diversity, coverage, metabolic and pathway analyses, tools for comparative metagenomics
  • Data standards and submission: European Nucleotide Archive (ENA), Genomic Standards Consortium (GSC), SRA, Webin
  • Public resources for metagenomics


Georg Zeller: