Genomics for working with pathogens (Brazil)


 Monday 26 Thursday 29 May 2014


Centro de Pesquisas René Rachou – Fundação Oswaldo Cruz - entro de Pesquisas René Rachou – Fundação Oswaldo Cruz, Av. Augusto de Lima, 1715, Belo Horizonte,  MG, 30190-002, United Kingdom

Application deadline: 

Monday 12 May 2014


Open application with selection


Johanna Langrish

Registration fee: 

R$ 300,00

Registration closed

Course Overview

This course will provide delegates with hands-on training in annotation genomes and accessing genomic information via the Ensembl Genomes browser, for those working in the area of pathogen genomes.  An overview of high throughput sequencing workflows and analysis (mainly using RNA-seq) will be presented, including introductions to the use of R and Bioconductor.



This course is aimed at PhD students and post-doctoral researchers who are working with pathogen genomes and wish to gain hands-on training in RNA-seq analysis and genome annotation. Familiarity with the technology and biological use cases of high throughput sequencing is required, and some experience with R/Bioconductor would be beneficial.

Learning outcomes

After this course you will be able to:

  • Search, query and retrieve genomic data from public repositories
  • Use bioinformatics tools to estimate gene expression levels
  • Discuss a variety of bioinformatic techniques for genome annotation


Time Topic Trainer
Day 1 - Monday 26 May 2014
09:00 Course introduction and overview Guilherme Corrêa de Oliveira
09:30 Overview of sequence data for genome annotation Gabriel da Rocha Fernandes
10:30 Tea/coffee break  
11:00 Lecture: Introduction to the high-throughput sequencing data analysis workflows, with examples from R Benilton Carvalho 
12:00 Lunch  
13:30 Practical: Introduction to Unix Gabriel da Rocha Fernandes
14:45 Practical: Introduction to R/Bioconductor Benilton Carvalho
15:30 Tea/coffee break  
16:00 Q&A Session  
17:15 End  
Day 2 - Tuesday 27 May 2014
09:00 Lecture: Estimating expression over genes and exons Gabriel da Rocha Fernandes
10:00 Tea/coffee break  
10:30 Practical: Estimating expression over genes and exons Gabriel da Rocha Fernandes
12:30 Lunch  
14:00 Lecture: Statistical concepts and methodologies for data analysis Benilton Carvalho
16:00 Tea/coffee break  
16:30 Practical: Statistical concepts and methodologies for data analysis Benilton Carvalho
17:30 Q&A session  
18:00 End  
Day 3 - Wednesday 28 May 2014
09:00 Genome alignments: Repeat masking, EST alignments & short read mapping (Introduction and hands-on)  Uma Maheswari 
10:30 Tea/coffee break  
11:00 Genome annotation: ab initio gene prediction, using expression data (EST and RNASeq), MAKER genome annotation  (Introduction and hands-on) Uma Maheswari 
12:00 Lunch  
13:30 Browsing Ensembl Protists (Introduction) Denise Carvalho-Silva 
14:00 Browser walkthrough Denise Carvalho-Silva 
15:30 Tea/coffee break  
16:00 Browser exercises  
16:30 Quick data access with BioMart (Introduction) Denise Carvalho-Silva 
17:00 BioMart exercises Denise Carvalho-Silva
18:30 End
Day 4 - Thursday 29 May 2014
09:00 Genome annotation (cont.) Uma Maheswari
10:30 Tea/coffee break  
11:00 SNP calling Uma Maheswari
12:00 Lunch  
13:30 Ensembl Protists browser: variation and VEP Denise Carvalho-Silva  
14:30 Variation exercises Denise Carvalho-Silva
15:30 Tea/coffee break  
16:00 Comparative Genomics (Introduction and Hands-on) Denise Carvalho-Silva  
17:00 Ensembl Protists Wrap up, feedback survey Denise Carvalho-Silva
18:00 Close of course Guilherme Corrêa de Oliveira