Pathogen Genomics: From NGS Data to Biological Complexity in Pathogen Variant Analysis
Overview: This workshop provides a structured and practical approach to pathogen genomics, enabling participants to process real-world sequencing data efficiently. By the end of the workshop, attendees will be well-equipped to perform variant calling, interpret genomic variants, and contribute to pathogen surveillance and outbreak investigations.
Sequence Alignment
Variant Calling
Pathogen Analysis
Genomic Survillance
5 coding
2 quizzes
Beginners
5 reading
5 wet-lab
Genomics
5 problems and applications
2 consulting and assessment sessions
Online, hands-on workshops
5 days (25 hours) to completed
2 Languages available (Arabic and English)
Scientists, bioinformaticians, and students
Workshop Structure
Day 1: Introduction to Pathogen Genomics
An overview of pathogen genomes (bacteria, viruses, fungi) and their role in infectious disease research. Topics include whole-genome sequencing, metagenomics, and applications in epidemixology and outbreak investigations.
Pathogen Genomics
Day 2: Sequence Alignment – Mapping Pathogen Genomes
Introduction to sequence alignment techniques and algorithms, including pairwise/multiple alignments and read mapping to reference geneome. Hands-on practice with quality control tools and alignments such as BWA, Bowtie2, and Minimap2 for aligning pathogen genomes to references.
Sequence Alignment
Day 3: Variant Calling – Identifying Pathogen Variants
Exploring SNP and indel detection in pathogens using next-flow workflows including, GATK, FreeBayes, and LoFreq. Participants will learn to process raw sequencing data, filter variants, and annotate their effects on pathogen behavior.
Variant Calling
Day 4: Pathogen Variant Analysis
This session delves into functional annotation of pathogen variants, phylogenetic analysis, and the use of comparative genomics to study pathogen evolution. Participants will work with annotation tools such as SnpEff and VEP, and explore pathogen phylogenetics with Nextstrain.
Pathogen Analysis
Day 5: Applications in Pathogen Genomics
The final day focuses on real-world applications of pathogen genomics, demonstrating how genomic data can be applied to epidemiology. Real-world applications.mIntroduction to AI-driven approaches in pathogen genomics and future directions.
Real-world applications