Table 4 Comparison of performance of different methods on reconstruction of three haplotypes for real kangaroo data sets from the mixture of reads [8] for (a) amplicon 1, (b) amplicon 2, and (c) amplicon 3
From: HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations
a. Amplicon 1 (total length of three haplotypes: 13921) | |||||
Software | # contigs | Longest | N50 | Haplotypes | Error rate % |
≥ 500bp | contig | coverage % | |||
HaploJuice | 3.0 ± 0.0 | 4613 ± 2.1 | 4612 ± 2.0 | 99.4 ± 0.0 | 0.05 ± 0.07 |
hmmfreq[8] | 3.0 ± 0.0 | 4485 ± 0.6 | 4484 ± 0.6 | 96.6 ± 0.0 | 0.26 ± 0.10 |
shoRAH[3] | 24.0 ± 2.6 | 4592 ± 7.0 | 4592 ± 6.0 | 95.6 ± 10.4 | 1.05 ± 0.32 |
SAVAGE[4] | 13.2 ± 2.1 | 903 ± 132.3 | 482 ± 169.6 | 47.3 ± 5.2 | 0.02 ± 0.04 |
PredictHaplo[5] | 1.1 ± 0.3 | 4630 ± 2.0 | 462 ± 1461.3 | 36.5 ± 10.5 | 0.01 ± 0.01 |
QuRe[6] | 4.0 ± 1.9 | 4343 ± 9.9 | 3909 ± 1373.7 | 74.9 ± 21.8 | 0.42 ± 0.32 |
b. Amplicon 2 (total length of three haplotypes: 12694) | |||||
Software | # contigs | Longest | N50 | Haplotypes | Error rate % |
≥ 500bp | contig | coverage % | |||
HaploJuice | 3.0 ± 0.0 | 4120 ± 1.5 | 4120 ± 1.5 | 97.4 ± 0.0 | 0.02 ± 0.03 |
hmmfreq[8] | 3.0 ± 0.0 | 3998 ± 4.0 | 3998 ± 4.0 | 94.5 ± 0.1 | 0.02 ± 0.01 |
shoRAH[3] | 24.2 ± 5.7 | 4119 ± 14.5 | 4118 ± 12.1 | 90.8 ± 13.5 | 0.41 ± 0.48 |
SAVAGE[4] | 8.8 ± 3.8 | 1806 ± 761.5 | 572 ± 81.7 | 50.2 ± 4.7 | 0.00 ± 0.00 |
PredictHaplo[5] | 2.0 ± 0.0 | 4140 ± 2.6 | 4136 ± 0.0 | 65.2 ± 0.0 | 0.00 ± 0.00 |
QuRe[6] | 2.4 ± 0.7 | 3746 ± 4.7 | 3373 ± 1185.0 | 38.4 ± 14.3 | 0.22 ± 0.28 |
c. Amplicon 3 (total length of three haplotypes: 15391) | |||||
Software | # contigs | Longest | N50 | Haplotypes | Error rate % |
≥ 500bp | contig | coverage % | |||
HaploJuice | 3.0 ± 0.0 | 5116 ± 9.1 | 5111 ± 7.7 | 99.6 ± 0.1 | 0.01 ± 0.00 |
hmmfreq[8] | 3.0 ± 0.0 | 5029 ± 3.1 | 5027 ± 3.6 | 98.0 ± 0.1 | 0.23 ± 0.11 |
shoRAH[3] | 27.6 ± 3.0 | 5132 ± 7.1 | 5111 ± 7.4 | 96.3 ± 10.5 | 1.91 ± 0.44 |
SAVAGE[4] | 11.8 ± 2.3 | 2510 ± 672 | 550 ± 40.4 | 55.6 ± 4.3 | 0.01 ± 0.01 |
PredictHaplo[5] | 1.6 ± 0.5 | 5170 ± 3.9 | 3070 ± 2642.4 | 53.3 ± 17.2 | 0.14 ± 0.09 |
QuRe[6] | 3.0 ± 1.1 | 4567 ± 2.1 | 4106 ± 1442.7 | 35.6 ± 12.5 | 0.25 ± 0.28 |