Population Genomics in Practice 2025
  • Slides
  • Exercises
  • Code recipes
  1. Exercises
  2. Simulation
  3. Listing
  • 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
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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
    • 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
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      • 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

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  • About
  • Listing
  1. Exercises
  2. Simulation
  3. Listing

Simulation index

List of exercises
Author

Per Unneberg

Published

18-Sep-2025

About

Collection of exercises related to simulation.

Listing

Title Description
HOWTO Start here: introduction to notebook setup.
Introduction to stdpopsim Introduction to simulations with stdpopsim
Simulating selection with stdpopsim Simulations of more complex scenarios with stdpopsim
Introduction to simulation with msprime Introduction to simulation with msprime
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2025 NBIS | GPL-3 License

 

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