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
Exercises
5E:
9E:
10E:
11E:
11E Excel sheet
Individual presentations
The present and future in AMR surveillance
Application of WGS in public health microbiology: Cholera and Haiti.
[3] 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
Phylogeny
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
Exercises:
2E: Investigating quality checks on isolated DNA
5E
9E: Using Enterobase
Individual presentations:
Introducing the workflow
Illumina Library Prep
Downloading Data
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
PyMoL
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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