Helminth Bioinformatics - Latin America & the Caribbean

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

Training Team

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

Matt Berriman
University of Glasgow, UK

Agustin Baricalla
CONICET, Argentina

Santiago Fontenla
Universidad de la República, Montevideo, Uruguay

Organisers

Alice Matimba
Wellcome Connecting Science, UK

Martin Aslett
Wellcome Connecting Science, UK

Karon Chappell
Wellcome Connecting Science, UK

Isabela Malta
Wellcome Connecting Science, UK

Vaishnavi Vikas Gangadhar
Wellcome Connecting Science, UK

Jack Monaghan
Wellcome Connecting Science, UK

Francesca Gale
Wellcome Connecting Science, UK

The course is open to scientists based in Latin America and the Caribbean, who are involved in helminth-related research.

Pre-requisites

Participants are required to take the Linux pre-course modules, which will be provided.

How to Apply

1. Start your application 
   • Click on the “Apply” button above to start your application. Please note that places are limited and will be awarded based on merit.
2. Demonstrate the course’s relevance to your work
   
   • Our courses are in high demand. Please provide an outline of your work (research project(s) and/ or clinical/ healthcare activities). It is essential to clearly explain how the skills you will acquire from the course are directly relevant to your current role and beneficial to your work, research, or organisation. Preference will be given to applicants who have genomic sequence data to analyse.
3. Letter of recommendation
   • Applications must be supported by a letter of recommendation from a sponsor or professional referee such as supervisor, line manager, or head of department. The statement should be tailored to indicate their  support of your application and how the course could be of benefit. This statement must be uploaded as a PDF document to the online registration system by the application deadline. Applications without a supporting statement will not be considered.
4. Need Help?
   • If you have any questions or encounter any problems with the online application process, please contact us for assistance.

The course is subsidised by Wellcome Connecting Science, and is free to attend.

Bursaries

Bursaries are offered based on merit to assist with accommodation, travel, and living expenses during the course. To apply, please complete the “bursary” section on the course application form. Recipients will typically be informed of their award in conjunction with their course acceptance.

Accommodation services phishing scam – please be vigilant. More information.

Attendee feedback from the 2023 course:

“I didn’t expect that I can understand the command line and genetic terminology in such a short period of time! This is amazing!”

“Apart from this course give really useful skills in bioformatics to me, fist time I don’t understand that why we have to use Linux and R in the bioinformatics field, and after finished I can understand and get the guideline to plan in my research in the future, that’s wonderful.”

“The topic was hard Science, but the course structure was well crafted. As a neophyte in Bioinformatics, I was not intimated by the content. Engaging and collaborating with other
Parasitology researchers was one of my favorite parts of this course. Thank you so much for your existence in this world Wellcome Connecting Science.”