Runyang Nicolas Lou, Arne Jacobs, Aryn Wilder, Nina O. Therkildsen
This GitHub repository contains our entire simulation and analysis pipeline. Below are links to markdown files containing the pipeline, and the shell scripts and SLiM scripts used in the pipeline are available in the shell_scripts
and slim_scripts
folder.
Simulation workflow with neutral simulation
Data analysis with neutral simulation and the Samtools GL model (including pool-seq comparison)
Data analysis with neutral simulation and the GATK GL model (including pool-seq comparison)
Simulation workflow with neutral simulation, with uneven input across individuals
Simulation workflow with spatially structured populations
Data analysis with spatially structured populations
Simulation workflow with spatially structured populations and lower migration rate
Data analysis with spatially structured populations and lower migration rate
Simulation workflow and data analysis with spatially structured populations and a longer chromosome
Simulation workflow with divergent selection
Data analysis with divergent selection simulation (including RAD-seq comparison)
Data acquisition and analysis with Heliconius butterflies
Simulation workflow with neutral simulation used for genotype imputation
Imputation without a reference panel
Figures for presentations and the paper