Metagenomics Bioinformatics


 Monday 2 Thursday 5 October 2017


European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Friday 05 May 2017

Application deadline: 

Friday 07 July 2017


Open application with selection

Registration fee: 

£430 including accommodation & food

Registration closed


This course will cover the use of publicly available resources to manage, share, analyse and interpret metagenomics data, including both marker gene and whole gene shotgun (WGS) 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 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:

Syllabus, tools and resources

During this course you will learn about:

  • 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


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


7Time Topic Trainer
Day 1 - 2nd October 2017
11:30 - 12:30 Registration and Lunch  
12:30 - 13:00 An introduction to EMBL-EBI Laura Emery
13:00 - 13:30 Sequencing technologies for metagenomics Alex Almeida
13:30 - 14:00 Introduction to metagenomics data analysis: provenance, reproducibility and workflows Alex Mitchell
14:00 - 15:00 Quality control (with hands on) Hubert Denise
15:00 - 15:30 Tea/coffee break  
15:30 - 17:00 Sequence and metadata submission to ENA  Jeena Rajan and Ana Toribio
17:00 Free time  
17:30 Dinner at Hinxton Hall  
Day 2 - 3rd October 2017
09:00 - 10:30 Taxonomic analysis and QIIME Morgan Langille
10:30 - 11:00 Tea/coffee break  
11:00 - 12:00 Taxonomic anlaysis and QIIME (cotd.) Morgan Langille
12:00 - 13:00 Lunch  
13:00 - 14:30 PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States Morgan Langille
15:00 - 15:30 Tea/coffee break  
15:30 - 17:30 Markers, reference databases, and other tools for taxonomic analysis. Alex Mitchell / Rob Finn
17:30 Free time  
18:00 Dinner at Hinxton Hall  
Day 3 - 4th October 2017
09:00 - 10:30 EBI Metagenomics: taxonomic and functional analysis Alex Mitchell / Ola Tarkowska
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 EBI Metagenomics (cotd.) Alex Mitchell / Ola Tartowska
12:30 - 14:30 Lunch and poster session  
14:30 - 15:30 Other platforms for metagenomics data analysis Rob Finn
15:30 - 16:00 Tea/coffee break  
16:00 - 17:30 Assembly and binning Rob Finn
17:30 Free time  
18:00 Dinner at Red Lion Hinxton  
Day 4 - 5th October 2017
09:00 - 11:00 Tools for comparative metagenomics  Georg Zeller
11:00 - 11:30 Tea/coffee break  
11:30 - 12:30 Estimating sequence diversity and coverage Tom Curtis
12:30 - 13:00 Course feedback and wrap up Laura Emery
13:00 Lunch   
13:45 Coach departs to Cambridge train station