Metagenomics Bioinformatics

Date:

 Tuesday 18 - Thursday 20 October 2016

Venue: 

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

Application opens: 

Friday 15 April 2016

Application deadline: 

Friday 22 July 2016

Participation: 

Open application with selection

Contact: 

EMBL-EBI Training Team

Registration fee: 

£175

Registration closed

Overview

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.

Audience

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.

Prerequisites

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

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 data analyses
  • Discuss the pitfalls and challenges in the field

Programme

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

At EMBL-EBI, we manage the world’s public biological data and make it freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. Set on the beautiful Wellcome Genome Campus near Cambridge in the UK, we support scientists throughout the world in seeking solutions to challenges in healthcare, agriculture and the environment.

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How to apply

In order to be considered for a place on this course, applicants must do the following:

  1. Complete the online application form.
  2. Submit a WORD document to johanna@ebi.ac.uk containing a short biography including your work history, a description of your current research interests and a short biography. Each document should be no longer than 100 words and written in paragraph form.
  3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course.

Further details will be provided on your confirmation email after completing the online form.

Incomplete applications will NOT be considered. Please read through the following guidance document for more information on how to complete your application.

Previous versions of the course can be viewed here

Application deadline

22 July 2016

Number of places

30 places

Registration closed

Organisers

Laura Emery

Rob Finn

Trainers

Laura Emery - EMBL-EBI, UK

Alex Mitchell - EMBL-EBI, UK

Rob Finn - EMBL-EBI, UK

Petra Ten Hoopen - EMBL-EBI, UK

Hubert Denise - EMBL-EBI, UK

Darren Wilkinson - University of Newcastle, UK

Tom Curtis - University of Newcastle, UK

Annalisa Mupo - EMBL-EBI, UK

Morgan Langille - Dalhousie University

Materials & attachments

Course materials