NGS Academy for the Africa CDC Pathogen Genomics Initiative

Pathogen Surveillance Training Curricula

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Module Code Pathogen Persona Module Title
B01 Foundational Bioinformatics Scientist Unix/linux, command line, shell scripting
B02 Foundational Bioinformatics Scientist Git and Version Control
B03 Foundational Bioinformatics Scientist Informatics skills
B04 Foundational Bioinformatics Scientist Programming in Python
B05 Foundational Bioinformatics Scientist R programming
B06 Foundational Bioinformatics Scientist Basic Data analytics
B07 Foundational Bioinformatics Scientist Phylogenetics
B08 Foundational Bioinformatics Scientist Software Containerisation
B09 Foundational Bioinformatics Scientist Workflow management systems
B10 Foundational Bioinformatics Scientist Ontologies, standards, data curation and submission
B11 Foundational Bioinformatics Scientist Ontologies, standards, data curation and submission
BA01 Bacterial Bioinformatics Scientist Introduction to bacterial NGS data processing
BA02 Bacterial Bioinformatics Scientist Bacterial pathogen data analysis
BA03 Bacterial Bioinformatics Scientist PATRIC
BA04 Bacterial Bioinformatics Scientist Phylogenetics
BA05 Bacterial Bioinformatics Scientist Metagenomics for pathogen surveillance
BA06 Bacterial Bioinformatics Scientist Data curation and submission
BA07 Bacterial Bioinformatics Scientist Dissemination of genomic surveillance findings
to policy makers and the public
001 Eukaryotic Bioinformatics Scientist Data analysis, interpretation, and presentation
002 Eukaryotic Bioinformatics Scientist Using data for decision-making, data sources for Malaria
003 Eukaryotic Bioinformatics Scientist Phylogenetics
004 Eukaryotic Bioinformatics Scientist Data curation and submission
W01 Foundational Wet-Lab Scientist only Basic laboratory health and safety protocols
W02 Foundational Wet-Lab Scientist only Basic laboratory requirements and operational set-up
W03 Foundational Wet-Lab Scientist only Introduction to fundamental laboratory skills and calculations
W04 Foundational Wet-Lab Scientist only Introduction to basic PCR techniques
V4 Viral Bioinformatics Scientist Introduction to Viral NGS Data Processing
V4a Viral Bioinformatics Scientist Nextclade and Pangolin
V4b Viral Bioinformatics Scientist Galaxy Workflow (or other selected workflow(s))
B07 Viral Bioinformatics Scientist Phylogenetics
V07 Viral Bioinformatics Scientist Advanced Bioinformatics Analysis for Viruses
B09 Viral Bioinformatics Scientist Ontologies, Standards, Data Curation and Submission
W01 Viral Wet-Lab Scientist only Basic Laboratory Health and Safety Protocols
W02 Viral Wet-Lab Scientist only Basic Laboratory Requirements and Operational Setup
W03 Viral Wet-Lab Scientist only Introduction to Fundamental Laboratory Skills and Calculations
W04 Viral Wet-Lab Scientist only Introduction to Basic PCR Techniques
V02 Viral Wet-Lab Scientist only Sample Processing and Library Preparation for Viral Pathogens (Theory and Wet-lab Practical)
V03 Viral Wet-Lab Scientist only ARTIC Viral Amplicon Sequencing
V03a Viral Wet-Lab Scientist only Illumina Workflow for Viral Genome Sequencing
V03b Viral Wet-Lab Scientist only ONT Workflow for Viral NGS Data processing
G02 Viral Wet-lab and Dry-lab Scientist Introduction to Genomic Epidemiology
G03 Viral Wet-lab and Dry-lab Scientist Introduction to Genomic Epidemiology and Pathogen Surveillance Modelling
V01 Viral Wet-lab and Dry-lab Scientist Introduction to Genomic Epidemiology
G05 Viral Wet-lab and Dry-lab Scientist Introduction to Genomic Sequencing and NGS
G06 Viral Wet-lab and Dry-lab Scientist Introduction to Genomic Data Dissemination
BA01 Bacterial Wet-Lab Scientist only Health and safety protocols
BA02 Bacterial Wet-Lab Scientist only Sample processing and library preparation
(Theory and wet lab practical)
BA03 Bacterial Wet-Lab Scientist only Lab practical: DNA sequencing
001 Eukaryotic Wet-Lab Scientist only Health and safety protocols
002 Eukaryotic Wet-Lab Scientist only Sample processing and library preparation
(Theory and wet lab practical)
003 Eukaryotic Wet-Lab Scientist only Lab practical: DNA sequencing
G01 Foundational Wet-lab and Dry-lab Scientist An Introduction to basic Genetics and Microbiology
G02 Foundational Wet-lab and Dry-lab Scientist Introduction to Epidemiology and Pathogen Surveillance
G03 Foundational Wet-lab and Dry-lab Scientist Introduction to Genomic Epidemiology and Pathogen Surveillance Modelling
G04 Foundational Wet-lab and Dry-lab Scientist Fundamentals of Genomic pathogen Surveillance Study Design
G05 Foundational Wet-lab and Dry-lab Scientist Introduction to Genomic Sequencing and NGS
G06 Foundational Wet-lab and Dry-lab Scientist Introduction to Public Health Research and Surveillance Ethics and Policies
G07 Foundational Wet-lab and Dry-lab Scientist Introduction to Data Sharing and Communication
G08 Foundational Wet-lab and Dry-lab Scientist Introduction to Antimicrobial Resistance
BA01 Bacterial Wet-lab and Dry-lab Scientist Introduction to genomic epidemiology
BA02 Bacterial Wet-lab and Dry-lab Scientist Study design for bacterial pathogen surveillance
BA03 Bacterial Wet-lab and Dry-lab Scientist Introduction to NGS
001 Eukaryotic Wet-lab and Dry-lab Scientist Introduction to Surveillance, Monitoring, and Evaluation.
Code Pathogen Persona Title