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Table 5 Comparison of SWER, MEC and runtimes for SDhaP and CPLEX on simulated diploid data with 5% error rate

From: SDhaP: haplotype assembly for diploids and polyploids via semi-definite programming

Data

Simulated data

 

SDhaP

CPLEX(optimal)

CPLEX(heuristic)

 

MEC

SWER

time

MEC

SWER

time

MEC

SWER

time

l 103, c 10

535

0.04

1

518

0.036

811

-

-

-

l 103, c 20

1042

0.007

4

-

-

-

1041

0.007

11393

l 103, c 30

1583

0.003

4

-

-

-

-

-

-

l 104, c 10

4971

0.099

14

4945

0.093

13800

7024

0.12

961

l 104, c 20

9839

0.0370

41

-

-

-

-

-

-

l 104, c 30

15310

0.0150

85

-

-

-

-

-

-

l 105, c 10

51342

0.210

375

-

-

-

-

-

-

l 105, c 20

102234

0.120

772

-

-

-

-

-

-

l 105, c 30

157234

0.030

1517

-

-

-

-

-

-

  1. MEC, SWER and running times (in seconds) for SDhaP, RefHap, HAPCUT and HapTree algorithms for simulated data of different lengths (l) and with different coverages (c). The data contains a fixed 5% fraction of genotyping errors. SDhaP is more accurate in terms of MEC and SWER and faster by almost an order of magnitude compared to other schemes for longer blocks.
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BMC Genomics

ISSN: 1471-2164

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