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Table 2 Comparison of GenHap and HapCol on the PacBio RS II dataset with covā‰ƒ30Ɨ

From: GenHap: a novel computational method based on genetic algorithms for haplotype assembly

   

GenHap

HapCol

f SNPs

cov

#SNPs

Avg HE

Std dev HE

Avg running time [s]

Avg HE

Std dev HE

Avg running time [s]

100

āˆ¼30Ɨ

500

2.04

0.59

0.11

2.42

0.78

2.24

  

1000

1.27

0.51

0.19

1.20

0.61

1.89

  

5000

1.06

0.19

0.94

0.60

0.17

9.04

  

10000

0.96

0.19

2.50

0.43

0.11

15.51

  

20000

1.02

0.14

8.49

0.41

0.11

31.13

200

āˆ¼30Ɨ

500

2.09

0.52

0.14

1.73

0.42

0.95

  

1000

1.70

0.24

0.22

1.09

0.41

1.84

  

5000

1.05

0.18

1.39

0.54

0.11

7.10

  

10000

1.13

0.18

4.09

0.51

0.17

14.13

  

20000

1.02

0.13

13.86

0.33

0.05

27.55

  1. The performances were evaluated both in terms of HE and running time
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BMC Bioinformatics

ISSN: 1471-2105

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