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Table 4 Running time of constructing kinship matrices based on genotypic data in PyAGH and GCTA

From: PyAGH: a python package to fast construct kinship matrices based on different levels of omic data

Number of individuals

PyAGH

GCTA

1000

10 s

2min32s

3000

51 s

2min36s

5000

1min39s

3min44s

10,000

4min50s

7min40s

  1. Both PyAGH and GCTA used all 64 threads of the machine for computation
  2. We fixing the number of snps at 1,000,000 while varying the numbers of individuals from 1,000 to 10,000
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BMC Bioinformatics

ISSN: 1471-2105

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