Day 1 WGS in AMR surveillance - presentation - pdf
Day 2 WGS in AMR surveillance - presentation - pdf
Day 3 WGS in AMR surveillance - presentation - pdf
Day 4 WGS in AMR surveillance - presentation - pdf
Day 5 WGS in AMR surveillance - presentation - pdf
Day 6 WGS in AMR surveillance - presentation - pdf
Recordings of each day:
Day 1 WGS in AMR surveillance - recording - video
Day 2 WGS in AMR surveillance - recording - video
Day 3 WGS in AMR surveillance - recording - video
Day 4 WGS in AMR surveillance - recording - video
Day 5 WGS in AMR surveillance - recording - video
Day 6 WGS in AMR surveillance - recording - video
11E Excel sheet
The present and future in AMR surveillance
Application of WGS in public health microbiology: Cholera and Haiti.
 Taking epidemiology into account –what to sequence and how much?
Overview of terminology and different sequencing platforms
Basic quality control of raw reads
Bioinformatics Basics: General introduction to bioinformatics and introducing genome assembly.
Online tools 1
Online tools 2
Online tools 3
Genotype to Phenotype
The Nagoya protocol
13-1 NICD, South Africa: Genomic surveillance of enteric pathogens
13-2 FDA, USA: Genomic and metagenomics based surveillance of AMR in the United States under the National Antimicrobial Resistance Monitoring System (NARMS)
13-3 DTU, Denmark: WGS surveillance in Europe
13-4 Africa Union/Africa CDC: Pathogen Genomics for Infectious Disease Control and Elimination in Africa
13-5 WHO: Integrated surveillance of AMR and the ESBL Ec tricycle project.
Day 1 presentation - pdf
Day 2 presentation - pdf
Day 3 presentation - pdf
Day 4 presentation - pdf
2E: Investigating quality checks on isolated DNA
Introducing the workflow
Illumina Library Prep
Recap on Bioinformatics
Recap on CGE Tools
Protocols and ISOs
Data Sharing Practices and Repositories
Data Sharing NCBI and Species
Day 1 presentation - pdf
Galaxy and Exatype Analysis
Example report for pipeline exercise
SARS-CoV-2 genomic surveillance- From respiratory sample to SARS-CoV-2 genome. Jinal Bhiman.
[5b] Library prep: COVIDSeq. Zama Khumalo.
[6a] Illumina sequencing NextSeq. Thabo and Zama.
Downloading data. Stanford Kwenda
Galaxy pipeline - Cathrine Scheepers
[11b] Introduction to PANGOLin and COVDB online tools - Daniel Amoako
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