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fastNGSadmix: admixture proportions and principal component analysis of a single NGS sample
Emil Jørsboe1, Kristian Hanghøj2,3, Anders Albrechtsen1
1Department of Biology, The Bioinformatics Centre, University of Copenhagen, 2200 Copenhagen N, Denmark.
Motivation:
Estimation of admixture proportions and principal component analysis (PCA) are fundamental tools in populations genetics. However, applying these methods to low- or mid-depth sequencing data without taking genotype uncertainty into account can introduce biases.
Results:
Here we present fastNGSadmix, a tool to fast and reliably estimate admixture proportions and perform PCA from next generation sequencing data of a single individual. The analyses are based on genotype likelihoods of the input sample and a set of predefined reference populations. The method has high accuracy, even at low sequencing depth and corrects for the biases introduced by small reference populations.
Availability And Implementation:
The admixture estimation method is implemented in C ++ and the PCA method is implemented in R. The code is freely available at http://www.popgen.dk/software/index.php/FastNGSadmix.
Contact:
emil.jorsboe@bio.ku.dk.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
