Wellcome Connecting Science Course Run Website
[Course Time Table 2025](coming soon)
Course Informatics Guide
Advancements in sequencing technologies have enabled the production of draft and high-quality genome assemblies for the most significant disease-causing helminths. However, the full potential of these data remains unrealised due to challenges in data manipulation and computational analyses, which often hinder their maximum benefit and accurate interpretation. This Helminth Bioinformatics course is designed to bridge that gap, empowering attendees with the skills to access, analyse, and present large-scale genomic data effectively.
What Will This Course Cover?
Through immersive, hands-on training, you will master key bioinformatics techniques, including read mapping, transcriptomics, phylogenetics, genome assembly and genetic variation analysis, all tailored to address the challenges presented by large helminth genomes. By the end of this course, you will not only have a toolkit of cutting-edge bioinformatics skills but also the confidence to overcome the challenges of large-scale genomic data.
In addition, the course integrates science engagement training into its curriculum, equipping you with the skills and confidence to communicate complex genomic concepts to non-specialist audiences. You will explore effective science communication approaches and work collaboratively to design and deliver a live engagement event for the local community. This practical experience will enhance your bioinformatics expertise and outreach capabilities.
Who should attend this course?
This course is aimed at postgraduate scientists including Masters and PhD Students, Postdoctoral Researchers, and healthcare professionals who may use genomics in their work. This week-long course is free to attend and open to applicants based in Latin America and the Caribbean involved in helminth-related research. The course will be taught in English.
What will you achieve?
After completing this course, you will be able to:
- utilise essential bioinformatics tools to format and manipulate helminth genomic data for various analysis workflows.
- use long read sequence data, taken from a sequencing machine, to perform downstream analyses.
- download, manage, and visualise large-scale helminth genomic data using genome browsers.
- map sequencing read data to a helminth reference genome and visualise using a genome browser.
- characterise helminth genomic variation, identifying SNP variants and other markers important for downstream analysis.
- construct phylogenetic trees to study evolutionary relationships among helminth samples.
- design experiments and analyse helminth transcriptomic data to interpret differential gene expression patterns.
- deliver engaging outreach activity for non-specialist genomics audiences.
The programme will cover several aspects of analysis of next generation sequencing data of helminth genomes. Sessions will include lectures, hands-on practical computational sessions, case studies and seminars.
Topics will include:
- Foundations in bioinformatics tools: Unix/Linux command-line operations and an introduction to R programming
- Introduction to the WormBase Parasite Database: Navigating this specialised resource for helminth genomic data.
- Genome Assembly: Building and interpreting genome assemblies, particularly for large and complex helminth genomes, using long-read sequencing techniques.
- Read mapping: Alignment of sequencing reads to reference genomes
- Variant Calling: Identifying genetic variations within populations to uncover meaningful biological insights.
- Transcriptomics: Explore gene expression patterns and analyse differential gene expression to understand functional genomics in helminths.
- Phylogenetics: Dive into evolutionary relationships, constructing phylogenetic trees to study helminth genomic diversity.
- Science engagement: Essentials of effectively communicating genomics to non-specialist audiences
Course Instructors
- Jose (Pepe) Tort, Universidad de la República, Montevideo, Uruguay
- Andres Iriarte, Universidad de la República, Montevideo, Uruguay
- Steve Doyle, Wellcome Sanger Institute, UK
- Laura Kamenetzky, Universidad de Buenos Aires
- Anna Protasio, University of Cambridge, UK
- Marina Papaiakovou, University of Cambridge, UK
- Matt Berriman, University of Glasgow, UK
- Agustin Baricalla, CONICET, Argentina
- Santiago Fontenla, Universidad de la República, Montevideo, Uruguay
Wellcome Connecting Science Team
- Alice Matimba, Head of Training and Global Capacity
- Karon Chapell, Events Organiser
- Isabela Malta, Assistant Overseas Courses Manager
- Monica Abrudan, Bioinformatics Education Developer
- Martin Aslett, Informatics Manager
- Vaishnavi Vikas Gangadhar, Informatics Technical Officer
- Jack Monaghan, Science Engagement Manager
- Francesca Gale, Head of Science Engagement and Enrichment
The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
Each course landing page is assigned a DOI via Zenodo, providing a stable and citable reference. These DOIs can be found on the respective course landing pages and can be included in CVs or research publications, offering a professional record of the course contributions.
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