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Table 3 Comparison of SWER, MEC and runtimes for different schemes on simulated diploid data

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

Data Simulated data
  SDhaP RefHap HAPCUT HapTree
  MEC SWER time MEC SWER time MEC SWER time MEC SWER time
l 103, c 10 86 0.002 4 123 0.009 8 123 0.009 6 123 0.009 31
l 103, c 20 212 0.001 5 293 0.010 169 303 0.011 8 305 0.006 14
l 103, c 30 300 0.001 7 378 0.007 567 377 0.002 7 378 0.001 14
l 104, c 10 1112 0.003 28 1257 0.008 2341 1354 0.011 282 1354 0.010 34905
l 104, c 20 2088 0.003 36 2659 0.008 36392 2774 0.009 680 2774 0.009 35443
l 104, c 30 3482 0.004 81 4164 0.009 39184 4277 0.010 604 4283 0.009 17002
  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 1% 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.