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Table 2 Comparison of GenHap and HapCol on the PacBio RS II dataset with cov30×

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 30× 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 30× 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