Population Genomics in Practice 2025
  • Slides
  • Exercises
  • Code recipes
  1. Welcome page
  • Slides
    • Listing
    • 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
      • Listing
      • DNA sequencing data
      • Read mapping
      • Variant calling and genotyping
      • Variant calling workflows
    • Variant filtering
      • Listing
      • Variant filtering
      • Depth filtering
    • Genetic diversity
      • Listing
      • Genetic diversity
    • Population structure
      • Listing
      • Principal component analysis
      • Admixture
    • Demography
      • Listing
    • Selection
      • Listing
    • Simulation
      • Listing
      • Brief introduction to simulation packages and stdpopsim
      • Primer on the coalescent and forward simulation
      • Ancestral recombination graph inference
  • Exercises
    • Listing
    • Data
      • Compute environment
      • Monkeyflowers dataset
    • Variant calling
      • Listing
      • Variant calling introduction
      • Data quality control
      • Read mapping and duplicate removal
      • Variant calling workflow
    • Variant filtering
      • Listing
      • Basic variant filtering
      • Depth filtering on invariant sites
    • Recombination and linkage
      • Listing
      • Linkage disequilibrium decay
    • Genetic diversity
      • Listing
      • Genetic diversity landscapes
    • Population structure
      • Listing
      • 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

Welcome page

Published

18-Sep-2025

Important

This website is work in progress.

2025 NBIS | GPL-3 License

 

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