Table 5 Evaluating the effects of different correcting strategies on diploid/polyploid genome sequencing data. In the completeness (%) multicolumn, all is the k-mer completeness for both haplotypes combined, matis maternal hap-mer completeness and pat is paternal hap-mer completeness. Switch error rate = the ratio of the number of switches between true and alternative haplotypes to the total number of variant positions
From: Hybrid-hybrid correction of errors in long reads with HERO
Datasets | QV | Error rate (%) | Completeness (%) | Switch error rate (%) | ||
|---|---|---|---|---|---|---|
Al | Mat | Pat | ||||
Arabidopsis thaliana | ||||||
PacBio reads | 10.56 | 8.78 | 89.54 | 80.05 | 79.89 | 47.80 |
Ratatosk | 13.83 | 4.14 | 99.04 | 97.89 | 97.84 | 15.38 |
R-HERO | 16.04 | 2.49 | 99.08 | 98.01 | 97.94 | 12.23 |
FMLRC | 15.07 | 3.11 | 97.10 | 92.33 | 92.05 | 17.81 |
F-HERO | 16.23 | 2.38 | 97.96 | 95.28 | 95.11 | 15.91 |
LoRDEC | 14.58 | 3.48 | 97.80 | 93.89 | 93.65 | 22.20 |
L-HERO | 15.94 | 2.55 | 98.43 | 95.94 | 95.76 | 18.70 |
Arctia plantaginis | ||||||
PacBio reads | 10.46 | 9.00 | 97.76 | 37.26 | 36.7 | 57.12 |
Ratatosk | 14.03 | 3.95 | 98.59 | 63.19 | 62.28 | 55.38 |
R-HERO | 19.49 | 1.12 | 99.67 | 68.02 | 67.02 | 54.14 |
FMLRC | 15.08 | 3.10 | 98.90 | 56.36 | 55.52 | 55.88 |
F-HERO | 19.27 | 1.18 | 99.71 | 65.92 | 65.03 | 54.19 |
LoRDEC | 15.86 | 2.60 | 98.86 | 58.89 | 58.00 | 54.73 |
L-HERO | 20.83 | 0.83 | 99.76 | 65.31 | 64.42 | 53.71 |
Oryza sativa japonica | ||||||
ONT reads | 13.47 | 4.50 | 91.14 | — | — | — |
Ratatosk | 19.41 | 1.14 | 98.37 | — | — | — |
R-HERO | 21.74 | 0.67 | 99.57 | — | — | — |
FMLRC | 20.85 | 0.82 | 98.26 | — | — | — |
F-HERO | 23.79 | 0.42 | 99.32 | — | — | — |
LoRDEC | 22.10 | 0.62 | 98.65 | — | — | — |
L-HERO | 25.70 | 0.27 | 99.41 | — | — | — |
Oryza sativa aromatic | ||||||
PacBio reads | 10.30 | 9.34 | 56.29 | — | — | — |
Ratatosk | 16.79 | 2.10 | 95.84 | — | — | — |
R-HERO | 19.83 | 1.04 | 99.37 | — | — | — |
FMLRC | 17.94 | 1.61 | 92.56 | — | — | — |
F-HERO | 21.99 | 0.63 | 98.11 | — | — | — |
LoRDEC | 19.35 | 1.16 | 95.50 | — | — | — |
L-HERO | 23.19 | 0.48 | 98.80 | — | — | — |
Mangifera indica | ||||||
PacBio reads | 10.40 | 9.11 | 96.78 | — | — | — |
Ratatosk | 17.99 | 1.59 | 99.94 | — | — | — |
R-HERO | 20.30 | 0.93 | 99.98 | — | — | — |
FMLRC | 19.85 | 1.04 | 99.86 | — | — | — |
F-HERO | 21.41 | 0.72 | 99.94 | — | — | — |
LoRDEC | 18.73 | 1.34 | 99.95 | — | — | — |
L-HERO | 21.34 | 0.73 | 99.98 | — | — | — |