Genomics for working with pathogens (Brazil)
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.
Syllabus, Tools and Resources
During this course you will learn about:
- Tools: Repeat masker, exonerate, SAMTools, VCFtools, Augustus, SNAP gene finder, MAKER and Apollo.
- Resources: Ensembl Genomes and BioMart
|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|
|11:00||Lecture: Introduction to the high-throughput sequencing data analysis workflows, with examples from R||Benilton Carvalho|
|13:30||Practical: Introduction to Unix||Gabriel da Rocha Fernandes|
|14:45||Practical: Introduction to R/Bioconductor||Benilton Carvalho|
|Day 2 - Tuesday 27 May 2014
|09:00||Lecture: Estimating expression over genes and exons||Gabriel da Rocha Fernandes|
|10:30||Practical: Estimating expression over genes and exons||Gabriel da Rocha Fernandes|
|14:00||Lecture: Statistical concepts and methodologies for data analysis||Benilton Carvalho|
|16:30||Practical: Statistical concepts and methodologies for data analysis||Benilton Carvalho|
|Day 3 - Wednesday 28 May 2014
|09:00||Genome alignments: Repeat masking, EST alignments & short read mapping (Introduction and hands-on)||Uma Maheswari|
|11:00||Genome annotation: ab initio gene prediction, using expression data (EST and RNASeq), MAKER genome annotation (Introduction and hands-on)||Uma Maheswari|
|13:30||Browsing Ensembl Protists (Introduction)||Denise Carvalho-Silva|
|14:00||Browser walkthrough||Denise Carvalho-Silva|
|16:30||Quick data access with BioMart (Introduction)||Denise Carvalho-Silva|
|17:00||BioMart exercises||Denise Carvalho-Silva|
|Day 4 - Thursday 29 May 2014
|09:00||Genome annotation (cont.)||Uma Maheswari|
|11:00||SNP calling||Uma Maheswari|
|13:30||Ensembl Protists browser: variation and VEP||Denise Carvalho-Silva|
|14:30||Variation exercises||Denise Carvalho-Silva|
|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|
Registration will be via a selection process. Incomplete applications will NOT be considered.
Application registration closes on Friday 9 May 2014 (12 noon GMT). Successful applicants will be notified by 16 May 2014.
NOTE: Participants will need to arrange their own travel to and from the course. If you require information regarding travelling to the venue or accommodation, please email admin
Successful applicants will be notified by e-mail and will then be asked to pay the course fee of R$ 300,00. The payment will be processed by the Brazilian Association of Bioinformatics and Computational Biology (AB3C) and detailed information regarding this payment will be given along with the notification email.