Table 2 Comparison of performance of different methods on reconstruction of three haplotypes for simulated data sets
From: HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations
a. Proportion of three samples: 0.5, 0.4, 0.1 (total length of three haplotypes: 30k) | |||||
Software | # contigs | Longest | N50 | Haplotypes | Error rate % |
≥ 500 bp | contig | coverage % | |||
HaploJuice | 3.0 ± 0.0 | 9975 ± 6.8 | 9971 ± 6.5 | 99.7 ± 0.0 | 0.001 ± 0.004 |
hmmfreq[8] | 3.0 ± 0.0 | 9855 ± 6.8 | 9850 ± 6.3 | 98.5 ± 0.0 | 0.276 ± 0.254 |
shoRAH[3] | 30.8 ± 11.7 | 9819 ± 124.8 | 9799 ± 116.7 | 97.5 ± 3.5 | 0.646 ± 0.492 |
SAVAGE[4] | 9.8 ± 3.5 | 9972 ± 11.8 | 305 ± 300.3 | 51.3 ± 7.1 | 0.001 ± 0.004 |
PredictHaplo[5] | 2.0 ± 0.2 | 9991 ± 4.2 | 9984 ± 5.6 | 67.7 ± 5.7 | 0.102 ± 0.034 |
QuRe[6] | 3.7 ± 1.9 | 6993 ± 1306.3 | 7374 ± 686.5 | 43.8 ± 13.5 | 0.331 ± 0.318 |
b. Proportion of three samples: 0.5, 0.3, 0.2 (total length of three haplotypes: 30k) | |||||
Software | # contigs | Longest | N50 | Haplotypes | Error rate % |
≥ 500bp | contig | coverage % | |||
HaploJuice | 3.0 ± 0.0 | 9975 ± 6.3 | 9971 ± 7.8 | 99.7 ± 0.0 | 0.000 ± 0.001 |
hmmfreq[8] | 3.0 ± 0.0 | 9854 ± 5.8 | 9850 ± 7.6 | 98.5 ± 0.0 | 0.089 ± 0.104 |
shoRAH[3] | 27.9 ± 6.6 | 9814 ± 118.3 | 9789 ± 113.9 | 97.1 ± 4.7 | 0.591 ± 0.358 |
SAVAGE[4] | 11.4 ± 3.4 | 9983 ± 8.2 | 436 ± 281.8 | 54.7 ± 7.1 | 0.001 ± 0.005 |
PredictHaplo[5] | 2.0 ± 0.2 | 9991 ± 3.7 | 9984 ± 5.8 | 68.0 ± 6.6 | 0.087 ± 0.040 |
QuRe[6] | 4.2 ± 2.2 | 7348 ± 820.8 | 7436 ± 776.9 | 44.9 ± 15.9 | 0.761 ± 0.851 |
c. Proportion of three samples: 0.6, 0.3, 0.1 (total length of three haplotypes: 30k) | |||||
Software | # contigs | Longest | N50 | Haplotypes | Error rate % |
≥ 500bp | contig | coverage % | |||
HaploJuice | 3.0 ± 0.0 | 9975 ± 7.3 | 9970 ± 7.7 | 99.7 ± 0.0 | 0.000 ± 0.000 |
hmmfreq[8] | 3.0 ± 0.0 | 9854 ± 5.6 | 9849 ± 6.2 | 98.5 ± 0.0 | 0.210 ± 0.214 |
shoRAH[3] | 25.2 ± 5.9 | 9837 ± 115.0 | 9808 ± 113.3 | 97.4 ± 4.8 | 0.749 ± 0.516 |
SAVAGE[4] | 11.2 ± 3.0 | 9971 ± 20.9 | 419 ± 260.5 | 53.9 ± 6.3 | 0.001 ± 0.006 |
PredictHaplo[5] | 2.0 ± 0.0 | 9991 ± 3.5 | 9984 ± 4.7 | 66.7 ± 0.0 | 0.089 ± 0.025 |
QuRe[6] | 3.9 ± 1.9 | 7074 ± 1284.4 | 7300 ± 716.6 | 39.1 ± 14.5 | 0.492 ± 0.597 |
d. Proportion of three samples: 0.7, 0.2, 0.1 (total length of three haplotypes: 30k) | |||||
Software | # contigs | Longest | N50 | Haplotypes | Error rate % |
≥ 500bp | contig | coverage % | |||
HaploJuice | 3.0 ± 0.0 | 9976 ± 6.1 | 9971 ± 6.3 | 99.7 ± 0.0 | 0.005 ± 0.048 |
hmmfreq[8] | 3.0 ± 0.0 | 9855 ± 6.2 | 9850 ± 6.7 | 98.5 ± 0.0 | 0.240 ± 0.220 |
shoRAH[3] | 20.2 ± 4.7 | 9835 ± 115.0 | 9812 ± 106.4 | 93.8 ± 11.2 | 0.912 ± 0.630 |
SAVAGE[4] | 15.2 ± 3.0 | 9974 ± 10.6 | 708 ± 161.7 | 65.1 ± 7.0 | 0.001 ± 0.005 |
PredictHaplo[5] | 2.0 ± 0.0 | 9991 ± 3.8 | 9984 ± 4.7 | 66.7 ± 0.0 | 0.088 ± 0.021 |
QuRe[6] | 3.6 ± 1.8 | 6787 ± 1333.0 | 7121 ± 809.6 | 28.4 ± 11.2 | 0.319 ± 0.535 |