Table 6.
Assembling the corrected reads using Canu. Assess the influence of different correction methods for diploid/polyploid genome assembly. 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 | |||||||
| Canu | Ratatosk | 22.87 | 0.52 | 66.55 | 40.31 | 40.31 | 8.59 |
| Canu | R-HERO | 23.86 | 0.41 | 70.13 | 43.05 | 43.05 | 7.94 |
| Canu | FMLRC | 23.63 | 0.43 | 61.46 | 32.51 | 32.29 | 11.34 |
| Canu | F-HERO | 23.88 | 0.41 | 61.89 | 33.01 | 32.10 | 11.17 |
| Canu | LoRDEC | 25.15 | 0.31 | 48.22 | 25.64 | 26.15 | 12.18 |
| Canu | L-HERO | 25.61 | 0.27 | 58.23 | 32.35 | 32.38 | 11.05 |
| Oryza sativa japonica | |||||||
| Canu | Ratatosk | 25.23 | 0.30 | 50.36 | — | — | — |
| Canu | R-HERO | 28.40 | 0.14 | 58.87 | — | — | — |
| Canu | FMLRC | 25.75 | 0.27 | 28.36 | — | — | — |
| Canu | F-HERO | 29.53 | 0.11 | 34.33 | — | — | — |
| Canu | LoRDEC | 25.88 | 0.26 | 30.28 | — | — | — |
| Canu | L-HERO | 29.83 | 0.10 | 54.27 | — | — | — |
| Oryza sativa aromatic | |||||||
| Canu | Ratatosk | 24.12 | 0.39 | 12.32 | — | — | — |
| Canu | R-HERO | 29.03 | 0.13 | 58.89 | — | — | — |
| Canu | FMLRC | 30.17 | 0.10 | 1.15 | — | — | — |
| Canu | F-HERO | 32.63 | 0.05 | 3.57 | — | — | — |
| Canu | LoRDEC | 25.76 | 0.27 | 4.38 | — | — | — |
| Canu | L-HERO | 29.94 | 0.10 | 41.28 | — | — | — |
| Mangifera indica | |||||||
| Canu | Ratatosk | 24.44 | 0.36 | 90.60 | — | — | — |
| Canu | R-HERO | 26.41 | 0.23 | 90.43 | — | — | — |
| Canu | FMLRC | 28.48 | 0.14 | 75.22 | — | — | — |
| Canu | F-HERO | 30.05 | 0.10 | 75.19 | — | — | — |
| Canu | LoRDEC | 24.67 | 0.34 | 61.46 | — | — | — |
| Canu | L-HERO | 26.88 | 0.21 | 70.09 | — | — | — |
Boldface is meant to indicate the best performing tool in the respective category