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

On this page

  • Code recipes
    • Slides
    • SLiM recipes
  1. Code recipes
  2. Code recipes

Code recipes

PGIP 2025 • Population Genomics in Practice

Published

18-Sep-2025

Code recipes

Important

Disclaimer: although the code posted here has at some point been used to generate figures and data, in some cases it may be out of date and not work out of the box. Please report any bugs or inconsistencies by posting an issue at https://github.com/NBISweden/workshop-pgip/issues.

Slides

Collection of recipes to generate data and figures for lecture notes. For full listing, see slides/index.html.

SLiM recipes

Collection of SLiM recipes (Haller, Ben, 2016) used to generate figures and examples. See slim/index.html for full listing.

References

Haller, Ben. (2016). Messer Lab SLiM. In Messer Lab. https://messerlab.org/slim/

2025 NBIS | GPL-3 License

 

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