Michael G. Campana, 2019
Smithsonian Conservation Biology Institute
CorrSieve helper scripts to calculate ΔK and perform Q-matrix correlations from ADMIXTURE output
The software is made available under the Smithsonian Institution terms of use.
Ruby scripts do not need to be compiled in advance. Simply clone the scripts, make them executable, and move them to a desired execution location.
git clone https://github.com/campanam/ADMIXTURE-stats
chmod +x ADMIXTURE-stats/*.rb
mv *.rb <destination>
The scripts (.rb) files can be executed locally using the ruby command or moved to a location within your $PATH. If in your path, simply invoke the script omitting the ruby command.
This script calculates Evanno et al.'s ΔK statistic for ADMIXTURE results. Input is a directory of ADMIXTURE log files and output are the ΔK results calculated as in CorrSieve (versions <= 1.7-0) in tab-separated values (TSV) format. Execution is:
ruby admixture_dK.rb <ADMIXTURE logs directory> > <deltaK results.tsv>
This script converts a directory of ADMIXTURE population assignment files (.Q) into rubyCorrSieve-readable (versions <= 1.7-0) input for Q-matrix correlations. WARNING: Converted files are not compatible with rCorrSieve. Execution is:
ruby convert_qmatrix.rb <ADMIXTURE .Q directory> <Output directory>
Output files can then be used by rubyCorrSieve for Q-matrix correlations, but will fail for other analyses.
Campana, M.G. 2019. ADMIXTURE-stats. https://github.com/campanam/ADMIXTURE-stats.
Campana, M.G. et al. 2011. CorrSieve: software for summarizing and evaluating Structure output. Mol. Ecol. Resour. 11:349-352. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1755-0998.2010.02917.x
Evanno et al. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14: 2611-2620. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2005.02553.x.
Alexandre et al. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19: 1655-1664. https://genome.cshlp.org/content/19/9/1655