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Training course in data analysis for genomic surveillance of African malaria vectors

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Workshop 1

Workshop 1 - Pyrethroid target-site resistance
Module 1 - Interactive cloud computing with Google Colaboratory
Module 2 - Accessing and exploring Anopheles genomic data
Module 3 - Navigating the Anopheles gambiae reference genome
Module 4 - Analysing SNPs in the Vgsc gene
Journal club - Clarkson et al. (2021)

Workshop 2

Workshop 2 - Metabolic insecticide resistance and copy number variation
Module 1 - Introduction to pandas DataFrames
Module 2 - The genetic basis of metabolic resistance to insecticides in Anopheles mosquitoes
Module 3 - Detecting CNVs from genome sequence data
Module 4 - Analysing CNV frequencies at metabolic resistance genes
Journal club - Lucas et al. (2019)

Workshop 3

Workshop 3 - Population structure
Module 1 - Plotting with Plotly Express
Module 2 - The biology of population structure
Module 3 - Genome-wide SNP data
Module 4 - Detecting population structure using PCA
Journal club - Ag1000G Consortium (2017)

Workshop 4

Workshop 4 - Cryptic species
Module 1 - NumPy arrays
Module 2 - Species complexes and cryptic taxa in malaria vectors
Module 3 - Ancestry-informative markers (AIMs)
Module 4 - Discovering cryptic taxa
Journal club - Tennessen et al. (2020)

Workshop 5

Workshop 5 - Genetic diversity
Module 1 - Xarray datasets
Module 2 - Introduction to genetic diversity
Module 3 - Genetic diversity summary statistics
Module 4 - Heterozygosity and runs of homozygosity

Workshop 6

Workshop 6 - Detecting genes under recent positive selection
Module 1 - Haplotypes
Module 2 - The biology of selective sweeps
Module 3 - Detecting new forms of insecticide resistance using selection scans
Module 4 - AnoPrimer - Primer Design in Anopheles gambiae

Workshop 7

Workshop 7 - Gene flow and the spread of insecticide resistance
Module 1 - Organophosphate resistance markers (combining SNP and CNV data)
Module 2 - Adaptive gene flow
Module 3 - Investigating gene flow at loci of interest using haplotype clustering
Module 4 - Investigating gene flow at loci of interest using haplotype networks

Workshop 8

Workshop 8 - Analysis planning and reporting
Module 1 - Planning a genomic surveillance exploratory data analysis
Module 2 - Presenting results of a genomic surveillance data analysis
Module 3 - Genomic surveillance of malaria vectors in Tanzania
Module 4 - Genomic surveillance of malaria vectors in Ghana

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By MalariaGEN and PAMCA

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