Table 1 Average runtimes of 10 initializations for both PCAngsd and NGSadmix
DatasetnmKPCAngsdNGSadmix (min)Depth (×)
Simulated3800.4 million32.9 min (2.1 min)7.9Embedded Image
1000 Genomes1938 million427.3 min (19.5 min)424.9Embedded Image
Waterbuck739.4 million514.5 min (9.3 min)192Embedded Image
  • The runtimes reported for PCAngsd include reading of data and estimation of covariance matrix and admixture proportions, while runtimes listed in parentheses only include estimation of admixture proportions, when parsing previously estimated individual allele frequencies. All tests have been performed server-side using 32 threads.