Population Genomics in Practice 2025
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  • Exercises
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  1. Slides
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  • Slides
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    • Introduction
      • Population genomics in practice
    • Population genetics foundations
      • Listing
      • Data and definitions
      • Alleles and genealogies
      • Linkage disequilibrium
      • The Wright-Fisher model
      • Genetic diversity
      • Selection
    • Variant calling
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      • DNA sequencing data
      • Read mapping
      • Variant calling and genotyping
      • Variant calling workflows
    • Variant filtering
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      • Variant filtering
      • Depth filtering
    • Genetic diversity
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      • Genetic diversity
    • Population structure
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      • Principal component analysis
      • Admixture
    • Demography
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    • Selection
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    • Simulation
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      • Brief introduction to simulation packages and stdpopsim
      • Primer on the coalescent and forward simulation
      • Ancestral recombination graph inference
  • Exercises
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    • Data
      • Compute environment
      • Monkeyflowers dataset
    • Variant calling
      • Listing
      • Variant calling introduction
      • Data quality control
      • Read mapping and duplicate removal
      • Variant calling workflow
    • Variant filtering
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      • Basic variant filtering
      • Depth filtering on invariant sites
    • Recombination and linkage
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      • Linkage disequilibrium decay
    • Genetic diversity
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      • Genetic diversity landscapes
    • Population structure
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      • Principal component analysis
      • Admixture
      • D-statistics
    • Simulation
      • Listing
      • HOWTO
      • Introduction to stdpopsim
      • Simulating selection with stdpopsim
      • Introduction to simulation with msprime
  • Code recipes
    • Code recipes
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Slides

PGIP 2025 • Population Genomics in Practice

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Slides

Title Description
Population genomics in practice Discussion of Fuller et al. (2020) to introduce concepts in population genomics.
Population genetics foundations Collection of short presentations on population genetic theory and foundations
Variant calling Collection of presentations on DNA sequencing and variant calling.
Variant filtering Collection of presentations on variant filtering.
Recombination and linkage Slides for recombination and linkage module.
Genetic diversity Collection of presentations on estimation of genetic diversity and related statistics.
Population structure Collection of presentations on the analysis of population structure
Selection Collection of presentations related to selection.
Demography Collection of presentations about demographic inference.
Simulation Collection of short presentations on simulation
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References

Fuller, Z. L., Mocellin, V. J. L., Morris, L. A., Cantin, N., Shepherd, J., Sarre, L., Peng, J., Liao, Y., Pickrell, J., Andolfatto, P., Matz, M., Bay, L. K., & Przeworski, M. (2020). Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching. Science, 369(6501), eaba4674. https://doi.org/10.1126/science.aba4674

2025 NBIS | GPL-3 License

 

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