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Table 5 Index scalability to the HPRC pangenome

From: Mem-based pangenome indexing for k-mer queries

# Genomes

MEMO-M

MEMO-C

KMC3-M

KMC3-C

PanKmer

9

0.33

0.34

128.19

15.41

14.57

18

0.59

0.59

256.31

15.85

15.58

27

0.81

0.80

384.42

16.21

16.54

36

0.97

0.95

512.58

16.48

17.39

45

1.16

1.13

654.98

16.79

18.36

54

1.36

1.31

768.88

17.11

19.36

63

1.57

1.51

897.07

17.43

20.40

72

1.94

1.74

1025.16

17.68

21.22

81

2.14

1.90

1153.31

17.87

22.44

89

2.35

2.04

1267.16

18.05

23.29

  1. Index sizes in GB of an increasing number of HPRC autosomal haplotypes. MEMO indexes are anchored to T2T-CHM13