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Table 1 Comparison of GenHap and HapCol on the Roche/454 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

0.04

0.08

0.21

0.00

0.00

0.62

  

1000

0.09

0.08

0.36

0.00

0.00

1.20

  

5000

0.18

0.06

3.17

0.01

0.03

5.35

  

10000

2.50

5.52

10.33

6.55

16.38

10.23

200

āˆ¼30Ɨ

500

0.09

0.14

0.34

0.00

0.00

0.50

  

1000

0.09

0.10

0.63

0.01

0.03

0.96

  

5000

3.61

3.43

6.07

0.38

0.78

4.90

  

10000

2.15

1.62

17.24

N/A

N/A

N/A

  1. The performances were evaluated both in terms of HE and running time. The N/A symbol denotes that HapCol was not able to complete the execution on all the 15 instances
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BMC Bioinformatics

ISSN: 1471-2105

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