Welcome to the official repository for the 5-Day Pathogen Genomics Workshop. This intensive course provides a hands-on journey from raw biological samples to actionable public health intelligence.
This workshop is tailored for professionals with limited bioinformatics experience, focusing on reproducible workflows using the Galaxy Interface. We cover the entire spectrum of pathogen genomics, including sequencing technologies, quality control, assembly, and antimicrobial resistance detection.
- Sequencing Literacy: Master the differences between Illumina and Nanopore technologies.
- Data Integrity: Perform rigorous Quality Control (QC) and filtering.
- Genome Reconstruction: Perform de novo assembly and annotation of bacterial genomes.
- Surveillance: Detect AMR genes and interpret phylogenetic relationships for outbreak tracking.
| Day | Topic | Key Tools | Resources |
|---|---|---|---|
| Day 1 | Foundations | Galaxy, NanoPlot | Guide |
| Day 2 | Quality Control | FastQC, Trimmomatic | Guide |
| Day 3 | Assembly & Annotation | Unicycler, Prokka | Guide |
| Day 4 | AMR Detection | StarAMR, ABRicate | Guide |
| Day 5 | Phylogenomics | Roary, Microreact | Guide |
- Agenda: Review the full Trainee Agenda.
- Assessment: Complete the Pre-Workshop Test.
- Setup: Ensure you have a registered account on UseGalaxy.com.
- Consult the Master Trainer Guide for detailed session breakdowns and filenames.
- Review the Trainer Agenda for time allocations and logistics.
- 🚀 Platform: Galaxy Training Network (GTN)
- 📚 Slides: Accessible in the
materials/subdirectories. - 🧪 Data: Links provided within the daily guides.
We stand on the shoulders of giants:
- WCSCourses: Slides and core modules are inspired by the NGS Bioinformatics 2025 team.
- Galaxy Training Network: Practical workflows are based on the globally recognized GTN tutorials.
This repository is for educational purposes. Please credit the original authors when reusing materials.