Overview and Objectives
The Pathogen Multiomics and Bioinformatics course is structured around seven distinct modules that span the entire spectrum from the introduction to NGS data and quality control to genome-wide association studies applied to different pathogens. The course comprehends a solid theoretical component that underpins the learning and execution of the different analytical stages, but it is, foremost, a practical hands-on course with the practical sessions comprising most of the course. It is intended that the participants apprehend the concepts and fundaments of the analytical procedures that are necessary to translate large data volumes generated by NGS platforms while systematically consolidating the theoretical basis of this knowledge.
The 2023 edition of this course will be taught in hybrid mode with simultaneous online and onsite sessions. All course material and a Virtual Machine containing all necessary software and datasets will be made available to all participants. Assistance towards VM deployment in local computers will be provided in advance. Furthermore, online interactive group sessions will be promoted for the discussion of results and networking between participants.
The program is structured across seven modules taking place between 03-07 July 2023.
Requirements: No requirements or pre-requisites are needed.
The course is credited with 6 ECTS.
Learning Topics and Skills to be Acquired by the Participants
The course program intendese tasks. In the end, the course participants should be able to:
- Understand, interpret and assess the different types and formats of data generated by NGS platforms as well as to perform quality-control steps;
- Map sequence data to a reference genome, identify variants on a genome-wide scale as well as performing its functional annotation;
- Carry out de novo assembly steps, including comparative analysis and genomic annotation;
- Integrate the previous analytical steps to genome-wide phylodynamic approaches aiming to study the evolution and dissemination of pathogens of public health importance;
- Perform transcriptomic analysis, evaluation and identification of differentially expressed genes;
- Characterize polymicrobial samples envisaging the assessment of its microbial composition and metagenome;
- Understand, interpret and perform Genome-Wide Association Studies (GWAS);
Programme and Schedule
03 July 2023 (Day 1)
09:00 – 13:00 Module 1 – Mapping, Visualization and Variant Calling
14:00 – 17:00 Module 2 – De novo Assembly
04 July 2023 (Day 2)
09:00 – 13:00 Module 3 – Pathogen Analytical Toolbox: Drug Resistance, Genotyping and Virulence
14:00 – 17:00 Module 4 – Introduction to Phylogenetics and Public Health (Part I)
05 July 2023 (Day 3)
09:00 – 13:00 Module 5 – Transcriptomics and RNA-Seq
14:00 – 17:00 Module 4 – Introduction to Phylogenetics and Public Health (Part II)
06 July 2023 (Day 4)
09:00 – 13:00 Module 6 – Metagenomic Analysis of Bacterial Populations
14:00 – 17:00 Module 7 – Genome-Wide Association Studies (GWAS)
07 July 2023 (Day 5)
09:00 – 16:00 Invited Guest Seminars (see here!)