Population Genomics in Practice 2025
Slides
Exercises
Code recipes
Welcome page
Slides
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Introduction
Population genomics in practice
Population genetics foundations
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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
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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
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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.