Bioinformatics for Infectious Disease Ecology Research (BInDER)
Practical Information
19-23 October 2026 - 09:00-12:00 : 13:30-17:30
University of Science and Technology of Hanoi (USTH), Hanoi, Vietnam http://usth.edu.vn/
Juliette Hayer / Tam Thi Thanh Tran
Course Description
đź“– Context
The University of Science and Technology of Hanoi (USTH) and the French National Research Institute for Sustainable Development (Institut de Recherche pour le Développement – IRD) in Montpellier, France, have established extensive research and training collaborations in the fields of microbiology, infectious disease ecology, and life sciences.
Within the framework of the cooperation between USTH and IRD, and with the aim of supporting training and enhancing research capacity among students, researchers, and early-career lecturers in Southeast Asia, USTH, in collaboration with IRD, is organizing the specialized course Bioinformatics for Infectious Disease Ecology Research.
The one-week specialized course consists of the following five modules:
High Throughput Sequencing: Quality Control and Assembly This course introduces the fundamentals of next-generation sequencing technologies and data processing. Participants will learn how to assess data quality, perform read trimming, and assemble genomes using short-, long-, and hybrid-read strategies. Practical sessions will focus on real datasets and the application of widely used bioinformatics tools for sequence assembly and visualization.
Genome Annotation and Bacterial/Viral Genomics Participants will learn how to annotate genomic sequences to identify genes, functional elements, and key biological features. Hands-on exercises will provide experience with annotation pipelines and genome visualization.
Comparative Genomics and Pangenomics This session focuses on understanding genetic diversity across multiple strains or species. Learners will perform comparative analyses to identify conserved and variable regions, construct core and accessory genomes, and interpret evolutionary relationships. The practical component will introduce pangenome analysis tools and data interpretation for microbiological insights.
Bacterial Metagenomics: metabarcoding and shotgun metagenomics This course covers the principles and workflows of metagenomic analysis, from raw data processing to microbial community profiling. Participants will learn how to analyse metabarcoding datasets (16S amplicons sequencing), assemble and classify bacterial genomes from complex environmental or clinical samples. Practical work includes taxonomic assignment, diversity analysis, and visualization of metagenomic datasets. Hands-on exercises will apply statistical methods to metagenomic datasets, enabling participants to generate meaningful summaries, plots, and interpretations of microbial community data.
Prerequisites
- Own a laptop.
- Have a galaxy account
- link to access the training group
Schedule
Monday 19/10/2026
| Time | Activity | Instructor(s) |
|---|---|---|
| 08:45-09:00 | Registration | |
| 09:00-09:30 | Welcome & Opening Session | Assoc. Prof. Nguyen Quang Huy, USTH Dr. Dorothée Misse, IRD Dr. Tran Thi Thanh Tam, USTH Dr. Juliette Hayer, IRD |
| 09:30-10:30 | Introduction to the research group and collaboration network | Assoc. Prof. Nguyen Quang Huy, USTH Dr. Dorothée Misse, IRD |
| 10:30-11:00 | Group photo & Coffee break | |
| 11:00-12:00 | Course 1: High Throughput Sequencing: Quality control, Assembly (short, long, hybrid) Introduction to Galaxy |
Dr. Tam Tran, USTH Dr. Mathis Arnal, IRD, Chiang Mai University |
| 12:00-13:30 | Lunch break | |
| 13:30-15:00 | Course 1: Practical session on quality control and de novo assembly | Dr. Tam Tran, USTH Dr. Mathis Arnal, IRD, Chiang Mai University |
| 15:00-15:30 | Coffee break | |
| 15:30-17:00 | Course 1: Practical session on quality control and de novo assembly | Dr. Tam Tran, USTH Dr. Mathis Arnal, IRD, Chiang Mai University |
Tuesday 20/10/2026
| Time | Activity | Instructor(s) |
|---|---|---|
| 09:00-10:30 | Course 1: Practical session on de novo assembly | Dr. Tam Tran, USTH Dr. Mathis Arnal, IRD, Chiang Mai University |
| 10:30-10:45 | Coffee break | |
| 10:45-12:00 | Course 2: Viral genomics (SARS-CoV2) - Concepts and practical session | Dr. Mathis Arnal, IRD, Chiang Mai University |
| 12:00-13:30 | Lunch break | |
| 13:30-15:00 | Course 2: Genome Annotation | Dr. Jacques Dainat, IRD |
| 15:00-15:30 | Coffee break | |
| 15:30-17:00 | Course 2: Practical session on annotation and bacterial genomics Antimicrobial Resistance (AMR) genes and virulence factors |
Dr. Jacques Dainat, IRD Dr. Juliette Hayer, IRD Dr. Praveen Rahi, Institut Pasteur du Cambodge |
Wednesday 21/10/2026
| Time | Activity | Instructor(s) |
|---|---|---|
| 09:00-10:00 | Course 3: Comparative genomics and pangenomics – theory and practice | Dr. Praveen Rahi, Institut Pasteur du Cambodge Dr. Juliette Hayer, IRD |
| 10:00-11:00 | Special Seminar | Dr. Jean-Christophe Auguet and Dr. Claudia Restrepo-OrtĂz, UMR MARBEC, UniversitĂ© Montpellier |
| 11:00-11:15 | Coffee break | |
| 11:15-12:00 | Course 3: Practical session on comparative genomics and pangenomics - phylogenomics | Dr. Praveen Rahi, Institut Pasteur du Cambodge Dr. Juliette Hayer, IRD |
| 12:00-13:30 | Lunch break | |
| 13:30-15:00 | Course 3: Practical session on comparative genomics and pangenomics – Panexplorer | Dr. Praveen Rahi, Institut Pasteur du Cambodge Dr. Jacques Dainat, IRD |
| 15:00-15:30 | Coffee break | |
| 15:30-17:00 | Course 4: Metabarcoding: theory | Dr. Jean-Christophe Auguet Dr. Tam Tran, USTH Dr. Mathis Arnal, IRD, Chiang Mai University |
Thursday 22/10/2026
| Time | Activity | Instructor(s) |
|---|---|---|
| 09:00-10:30 | Course 4: 16S Metabarcoding – practice | Dr. Mathis Arnal, IRD, Chiang Mai University Dr. Tam Tran, USTH |
| 10:30-10:45 | Coffee break | |
| 10:45-12:00 | Course 4: 16S Metabarcoding – practice | Dr. Mathis Arnal, IRD, Chiang Mai University Dr. Tam Tran, USTH |
| 12:00-13:30 | Lunch break | |
| 13:30-15:00 | Course 4: Shotgun Metagenomics – theory and practice | Dr. Juliette Hayer, IRD Dr. Mathis Arnal, IRD, Chiang Mai University |
| 15:00-15:30 | Coffee break | |
| 15:30-17:00 | Course 4: Shotgun Metagenomics – theory and practice | Dr. Juliette Hayer, IRD Dr. Mathis Arnal, IRD, Chiang Mai University |
Friday 23/10/2026
| Time | Activity | Instructor(s) |
|---|---|---|
| 09:00-10:30 | Course 4: Shotgun Metagenomics – theory and practice | Dr. Juliette Hayer, IRD Dr. Mathis Arnal, IRD, Chiang Mai University |
| 10:30-10:45 | Coffee break | |
| 10:45-12:00 | Course 4: Data exploration for Metagenomics – theory and practice | Dr. Tam Tran, USTH Dr. Juliette Hayer, IRD |
| 12:00-13:30 | Lunch break | |
| 13:30-15:00 | Additional: How to use/make a workflow on Galaxy? | Dr. Mathis Arnal, IRD, Chiang Mai University Dr. Tam Tran, USTH |
| 15:00-15:30 | Coffee break | |
| 15:30-17:00 | Summary of the workshop, questions, certificates | All |
The above schedule is approximate; variations may occur.
Teachers
| Name | Insitute | Role |
|---|---|---|
| Juliette Hayer | IRD, Montpellier, France | Course Coordinator / Instructor |
| Tam Thi Thanh Tran | USTH, Hanoi, Vietnam | Course Coordinator / Instructor |
| Jacques Dainat | IRD, Montpellier, France | Instructor |
| Mathis Arnal | Chang Mai University, Thailand | Instructor |
| Praveen Rahi | Institut Pasteur du Cambodge, Phnom Penh, Camdodia | Instructor |
| Huong Minh Huynh | USTH, Hanoi, Vietnam | Teaching assistant |
| Thu Minh Nguyen | USTH, Hanoi, Vietnam | Teaching assistant |