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1 Description

1.1 Introduction

This manual describes Genesis, a program created for scientists to generate PCA (Principal Component Analysis) and structure/admixture graphs from data outputted by common tools such as eigenstrat [Pritchard et al. 2000] and the SNPRelate [Zheng et al 2012] package for PCAs and Admixture [Alexander et al. 2009] and CLUMPP [Jakobsson and Rosenberg 2007] for admixtures.

Genesis was developed with user-friendliness in mind as other tools can be complex to use and lack certain features. All elements of the graphs that would need to be edited can be done so using a graphical user Interface where the graphs themselves are interactive and different elements can be viewed and changed at the click of the mouse. All this saves the time that scientists would rather be spending doing more important things.

Principal Component Analysis is a mathematical and statistical procedure that can used to analyse genotype data. The differences between samples' genotype data can be used to project each sample into a p-dimensional space, where the p axes are uncorrelated. For realistic data, typically p is 4 or less and often only the most important two demsnions are used. Programs such as eigenstrat produce the the PCs, and Genesis produces them. An example is found below:

pca.jpg

Admixture mappings are used to analyse populations of mixed ancestry and determine the ratios of proposed different ancestries. These ratios can then displayed in stacked bar graphs as structure/admixture graphs.

admix.jpg

1.2 Assumptions

This manual assumes that the reader is familiar with structure and PCA analysis of genotype data, and has used tools such as admixture, Eigenstrat and/or plink [Purcell et al 2007; Purcell and Chang 2014].

1.3 Licence

Genesis was written by Robert W Buchmann, and copyright is owned by the University of the Witwatersrand, Johannesburg. The code is released under the Affero General Public Licence version 3. Genesis uses the iText Software Corporation's iText library also released under the Affero General Public Licence.