Metagenomics Bioinformatics


 Tuesday 18 Thursday 20 October 2016


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

Application opens: 

Friday April 15 2016

Application deadline: 

Friday July 22 2016


Open application with selection

Registration fee: 


Registration closed

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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. 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)
  • Data analysis: The EBI Metagenomics Portal, QIIME, HMMER, InterPro, GO, FASTQC, diversity, coverage, sample comparisons, metabolic and pathway analyses
  • Data standards and submission: European Nucleotide Archive (ENA), Genomic Standards Consortium (GSC), SRA, Webin
  • Public repositories: MG Portal, MG-RAST


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 data analyses
  • Discuss the pitfalls and challenges in the field


Time Topic Trainer
Day 1 – Tuesday 18th October 2016 – Metagenomics introduction
09:30 - 10:00 Arrival, registration and tea/coffee  
10:00 - 10:30 An introduction to the EBI Annalisa Mupo
10:30 - 11:30 An introduction to sequencing technologies for metagenomics Matt Clark
11:30 - 12:00 Introduction to metagenomics data analysis: provenance, reproducibility & workflows Alex Mitchell
12:00 - 12:30 Public resources for metagenomic data analysis Rob Finn
12:30 - 13:30 Lunch  
13:30 - 15:00

Data standards and ENA data submission (with hands-on)

Petra ten Hoopen
15:00 - 15:30 Tea/coffee break  
15:30 - 17:00

Coupling different meta-omics approaches

Rob Finn, open discussion

17:00 - 19:00 Poster session  
19:00 Evening meal Hinxton hall
Day 2 – Wednesday 19th October 2016 – Taxonomic and functional analysis
09:00 - 10:00 Quality control with hands on Hubert Denise
10:00 - 11:00 Taxonomic analyses and QIIME hands-on Morgan Langille
11:00 - 11:30 Tea/coffee break  
11:30 - 13:00 Taxonomic analyses and QIIME hands-on (continued) Morgan Langille
13:00 - 14:00 Lunch and poster session  
14:00 - 16:00 EBI Metagenomics portal: taxonomic and functional analysis and hands-on Alex Mitchell
16:00 - 16:30 Tea/coffee break  
16:30 - 18:00 Data analysis with R Blaise Alako
19:00 Evening meal Hinxton hall
Day 3 – Thursday 20th October 2016 – Advanced analyses
09:00 - 10:30 Additional analysis tools (extending beyond EBI Metagenomics) Rob Finn
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 Estimating sequence diversity and coverage (hands-on) Darren Wilkinson/Tom Curtis
12:30 - 13:30 Lunch  
13:30 - 15:00 PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (hands on)    Morgan Langille
15:00 - 15:30 Course feedback and wrap up Annalisa Mupo
16:00 Coach to Cambridge Train Station