Table 7.
Assembling the corrected reads using HiFiasm-meta. 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
| Assembler | Data | QV | Error rate (%) | Completeness (%) | Switch error rate (%) | ||
|---|---|---|---|---|---|---|---|
| All | Mat | Pat | |||||
| Arabidopsis thaliana | |||||||
| Hifiasm-meta | Ratatosk | 23.55 | 0.44 | 35.31 | 16.77 | 16.64 | 10.49 |
| Hifiasm-meta | R-HERO | 22.71 | 0.54 | 36.77 | 18.06 | 18.45 | 10.58 |
| Hifiasm-meta | FMLRC | 33.93 | 0.04 | 8.36 | 3.32 | 4.55 | 7.58 |
| Hifiasm-meta | F-HERO | 24.49 | 0.36 | 19.23 | 8.58 | 9.44 | 8.80 |
| Hifiasm-meta | LoRDEC | 23.06 | 0.49 | 34.18 | 17.95 | 18.66 | 7.34 |
| Hifiasm-meta | L-HERO | 24.75 | 0.34 | 44.04 | 25.99 | 25.28 | 6.78 |
| Arctia plantaginis | |||||||
| Hifiasm-meta | Ratatosk | 20.51 | 0.89 | 8.45 | 0.05 | 0.04 | 53.60 |
| Hifiasm-meta | R-HERO | 21.30 | 0.74 | 11.77 | 0.15 | 0.15 | 50.82 |
| Hifiasm-meta | FMLRC | 23.28 | 0.47 | 0.22 | 0.01 | 0.00 | 46.67 |
| Hifiasm-meta | F-HERO | 22.33 | 0.59 | 49.65 | 2.55 | 2.50 | 53.27 |
| Hifiasm-meta | LoRDEC | 16.40 | 2.29 | 4.04 | 0.07 | 0.07 | 49.91 |
| Hifiasm-meta | L-HERO | 21.70 | 0.68 | 48.35 | 2.63 | 2.57 | 52.33 |
| Oryza sativa japonica | |||||||
| Hifiasm-meta | Ratatosk | 22.46 | 0.57 | 11.06 | — | — | — |
| Hifiasm-meta | R-HERO | 25.84 | 0.26 | 26.59 | — | — | — |
| Hifiasm-meta | FMLRC | 23.28 | 0.47 | 4.23 | — | — | — |
| Hifiasm-meta | F-HERO | 27.31 | 0.19 | 27.25 | — | — | — |
| Hifiasm-meta | LoRDEC | 21.42 | 0.72 | 19.91 | — | — | — |
| Hifiasm-meta | L-HERO | 24.23 | 0.38 | 39.96 | — | — | — |
| Oryza sativa aromatic | |||||||
| Hifiasm-meta | Ratatosk | 21.88 | 0.65 | 2.26 | — | — | — |
| Hifiasm-meta | R-HERO | 23.93 | 0.41 | 22.95 | — | — | — |
| Hifiasm-meta | FMLRC | 19.75 | 1.06 | 3.10 | — | — | — |
| Hifiasm-meta | F-HERO | 25.30 | 0.30 | 31.03 | — | — | — |
| Hifiasm-meta | LoRDEC | 18.62 | 1.37 | 7.19 | — | — | — |
| Hifiasm-meta | L-HERO | 23.74 | 0.42 | 37.20 | — | — | — |
| Fragaria x ananassa | |||||||
| Hifiasm-meta | Ratatosk | 21.35 | 0.73 | 75.29 | — | — | — |
| Hifiasm-meta | R-HERO | 23.14 | 0.49 | 81.44 | — | — | — |
| Hifiasm-meta | FMLRC | 19.60 | 1.10 | 21.53 | — | — | — |
| Hifiasm-meta | F-HERO | 23.14 | 0.49 | 42.45 | — | — | — |
| Hifiasm-meta | LoRDEC | 19.77 | 1.06 | 49.73 | — | — | — |
| Hifiasm-meta | L-HERO | 22.69 | 0.54 | 60.10 | — | — | — |