Metagenomics Bioinformatics, Brazil 2014

Date:

 Monday 3 Wednesday 5 November 2014

Venue: 

Universidade Católica de Brasília - Universidade Católica de Brasília, , Campus Avançado Asa Norte, Brasília,  - DF,  71966-700, Brazil

Application opens: 

Wednesday 01 October 2014

Application deadline: 

Thursday 16 October 2014

Participation: 

Open application with selection

Contact: 

Frank O’Donnell

Registration fee: 

R$100,00

Registration closed

Course Overview

This course will provide an introdution to the use of publicly available resources for the management, sharing, analysis and interpretation of metagenomics data, including both marker gene and whole gene shotgun (WGS) approaches. Delegates will gain hands-on experience of a range of data resources and tools, interspersed with lectures. Please note that it will not be possible to bring your own data for analysis during the course.

Audience

This course is aimed at wet-lab biologists who are starting out in the field of metagenomics research.

Prerequisites

Practical sessions in the course require a basic understanding of the Unix command line. Please ensure that you complete these free tutorials before you attend the course:

In addition, familiarity with the R statistical package, would be an advantage.

Learning outcomes

After this course you should be able to:

  • Comprehend the minimum standards required for data submission to comply with the Genomic Standards Consortium (GSC)
  • Understand the principals behind amplicon-based (marker gene) and functional analysis of metagenomic sequence data
  • Use a range of analysis tools, including the EBI metagenomics portal
  • Interpret results and compare them with other metagenomic datasets

Programme

Time Topic Trainer
Day 1 - 3rd November 2014
09:15 - 09:30 Registration  
09:30 - 10:00 Introduction and course expectations Gabriel Fernandes
10:00 - 10:30 Introduction to NGS Gabriel Fernandes
10:30 - 11:00 Tea/coffee break  
11:00 - 12:00 Considerations for metagenomics data analysis and summmary of workflows Alex Mitchell
12:00 - 13:00 Lunch  
13:00 - 14:00 Public data resources for metagenomics Hubert Denise 
14:00 - 15:30 Describing your data using standards. Peter Sterk
15:30 - 16:00 Tea/coffee break  
16:00 - 16:30 Command line warm up Alex Mitchell
16:30 - 17:30 Participant presentations All
Day 2 - 4th November 2014
09:00 - 10:30 Quality control  Hubert Denise
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 Taxonomic analysis of amplicon and shotgun data Peter Sterk
12:30 - 13:30 Lunch  
13:30 - 15:30 Taxonomic analyses: Qiime tutorial Peter Sterk
15:30 - 16:00 Tea/coffee break  
16:00 - 17:00 Taxonomic analyses: Qiime tutorial (Continued) and data visualisation using Emperor and Cytoscape Peter Sterk
17:00 - 18:00 Keynote TBC
Day 3 - 5th November 2014
09:00 - 09:30 InterPro and GO for functional analysis of metagenomic data Alex Mitchell 
09:30 - 11:00 Functional analysis using EMG Alex Mitchell
11:00 - 11:30 Tea/coffee break  
11:30 - 13:00 Analysis of metagenomics data using R Hubert Denise
13:00 - 14:00 Lunch  
14:00 - 15:00 Implementing Metagenomics workflows with Taverna / Galaxy Gabriel Fernandes
15:00 - 15:30 Suggestions for implementing metagenomics bioinformatics and Q&A All
15:30 - 16:00 Course feedback and wrap-up Gabriel Fernandes
16:00 Course close