NGS Academy for the Africa CDC Pathogen Genomics Initiative

Pathogen Surveillance Training Curricula

Click here for the training survey
The NGS Academy forms part of the Africa CDC Pathogen Genomics Initiative (PGI). This initiative is funded by the Bill & Melinda Gates Foundation. Our training initiatives are carried out in partnership with the African Society for Laboratory Medicine (ASLM).
Module code Pathogen Persona Module Title
Module Code Pathogen Persona Module Title
001 Foundational Bioinformatics Scientist Unix/linux, command line, shell scripting
002 Foundational Bioinformatics Scientist Data analytics
003 Foundational Bioinformatics Scientist Phylogenetics
004 Foundational Bioinformatics Scientist Informatics skills
005 Foundational Bioinformatics Scientist Workflows and containerization
006 Foundational Bioinformatics Scientist Programming in Python
007 Foundational Bioinformatics Scientist R programming
008 Foundational Bioinformatics Scientist Github and version control
009 Foundational Bioinformatics Scientist Ontologies, standards, data curation and submission
001 Viral Bioinformatics Scientist Introduction to NGS data processing
002 Viral Bioinformatics Scientist NGS, Illumina, ONT workflows
003 Viral Bioinformatics Scientist Nextclade and Pangolin
004 Viral Bioinformatics Scientist Galaxy workflow (or other slected workflow(s))
005 Viral Bioinformatics Scientist Phylogenetics
006 Viral Bioinformatics Scientist Advanced bioinformatics analysis for viruses
007 Viral Bioinformatics Scientist Data curation and submission
008 Viral Bioinformatics Scientist Dissemination of genomic surveillance findings
to policy makers and the public
001 Bacterial Bioinformatics Scientist Introduction to bacterial NGS data processing
002 Bacterial Bioinformatics Scientist Bacterial pathogen data analysis
003 Bacterial Bioinformatics Scientist PATRIC
004 Bacterial Bioinformatics Scientist Phylogenetics
005 Bacterial Bioinformatics Scientist Metagenomics for pathogen surveillance
006 Bacterial Bioinformatics Scientist Data curation and submission
007 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
001 Foundational Wet-Lab Scientist only Health and safety protocols
002 Foundational Wet-Lab Scientist only Lab practical: DNA/RNA sequencing
001 Viral Wet-Lab Scientist only Lab practical: RNA/DNA sequencing
002 Viral Wet-Lab Scientist only ARTIC amplicon sequencing
001 Bacterial Wet-Lab Scientist only Health and safety protocols
002 Bacterial Wet-Lab Scientist only Sample processing and library preparation
(Theory and wet lab practical)
002 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
001 Foundational Wet-lab and Dry-lab Scientist Ethics and policies
002 Foundational Wet-lab and Dry-lab Scientist Study design
003 Foundational Wet-lab and Dry-lab Scientist Dissemination of results
001 Viral Wet-lab and Dry-lab Scientist Introduction to genomic epidemiology
002 Viral Wet-lab and Dry-lab Scientist Study design for viral pathogen surveillance
003 Viral Wet-lab and Dry-lab Scientist Introduction to NGS
001 Bacterial Wet-lab and Dry-lab Scientist Introduction to genomic epidemiology
002 Bacterial Wet-lab and Dry-lab Scientist Study design for bacterial pathogen surveillance
002 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