Metagenomics Bioinformatics

Date:

 Tuesday 17 Friday 20 July 2018

Venue: 

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

Application opens: 

Monday 15 January 2018

Application deadline: 

Friday 13 April 2018

Participation: 

Open application with selection

Contact: 

Emily Rees

Registration fee: 

£430 including accommodation & food

Registration closed

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Overview

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.

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 may 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. 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

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

Programme

Time Topic Trainer
Day 1 - Tuesday 17th July 2018
11:30 - 12:30 Registration and lunch  
12:30 - 13:00 An Introduction to the EBI  Alexandra Holinski
13:00 - 13:30 Sequencing technologies for metagenomics  Michael Quail
13:30 - 14:00 Introduction to metagenomics data analysis: why provenance matters Alex Mitchell 
14:00 - 15:00 Quality control  Hubert Denise
15:00 - 15:30 Tea/coffee break  
15:30 - 17:00 Markers, reference databases and genes for taxonomic analysis Rob Finn 
17:00 - 17:30 Free time   
17:30  Dinner at Hinxton Hall  
Day 2 - Wednesday 18th July 2018
09:00 - 10:30 Taxonomic analysis and MAPseq Joao Mataias Rodrigues 
10:30 - 11:00 Tea/coffee break  
11:00 - 12:00 Taxonomic analysis and MAPseq (ctd) Joao Mataias Rodrigues 
12:00 - 13:00 Lunch  
13:00 - 15:00 EBI metagenomics with hands on   Alex Mitchell and Ola Tarkowska 
15:00 - 15:30 Tea/coffee break   
15:30 - 17:30 EBI metagenomics with hands on (ctd) Alex Mitchell and Ola Tarkowska 
17:30 - 18:00  Free time  
18:00  Dinner at Hinxton Hall  
Day 3 - Thursday 19th July 2018
09:00 - 10:30 Sequence and metadata submission ENA Jeena Rajan & Clara Amid 
10:30 - 11:00 Tea/coffee break  
11:00 - 11:30 Other analysis platforms Rob Finn
11:30 - 12:30 Searching the metagenomics peptide database Rob Finn 
12:30 - 14:00 Lunch and poster session   
14:00 - 15:30 Assembly and binning with hands-on Rob Finn & Alex Mitchell 
15:30 - 16:00 Break   
16:00 - 17:30 Co-assembly and species/strain resolution Chris Quince
17:30 Free time  
18:00 Dinner at Red Lion Hinxton  
Day 4 - Friday 20th July 2018
09:00 - 10:00 Estimating sequence diversity and coverage  Darren Wilkinson
10:00 - 11:00 Tools for comparative metagenomics Georg Zeller 
11:00 - 11:30 Tea/coffee break   
11:30 - 13:00 Tools for comparative metagenomics (ctd) Georg Zeller 
13:00 - 13:30 Course feedback and wrap up  Alexandra Holinski 
13:30 Lunch  
14:15 Coach departs for Cambridge train station