Table 4.
Results on assembly using Hifiasm-meta after correction by different correction protocols of PacBio CLR and ONT reads from 4 different real datasets. 1st column: genome assembly program = Hifiasm-meta. 2nd column: Error correction protocol. Ratatosk, FMLRC, and LoRDEC refer to 8 iterations of the respective methods (pointed out as optimal protocol earlier); R-HERO, F-HERO, and L-HERO refer to 3 iterations of Ratatosk, FMLRC, and LoRDEC, respectively, followed by 5 iterations of HERO-OG. Indels/100 kbp: average number of insertion or deletion errors per 100,000 aligned bases. Mismatches/100 kbp = average number of mismatch errors per 100,000 aligned bases. Genome fraction (GF) reflects how much of each of the strain-specific genomes is covered by the corrected reads. N/100 kbp denotes the average number of uncalled bases (Ns) per 100,000 bases in the read. MC = fraction of misassembled contigs
| Assemblers | GF(%) | Indels/100 kbp | Mismatches/100 kbp | NGA50 | N/100 kbp | MC (%) | |
|---|---|---|---|---|---|---|---|
| Bmock12 ONT | |||||||
| Hifiasm-meta | Ratatosk | 72.24 | 13.52 | 80.91 | 124596 | 0.19 | 5.85 |
| Hifiasm-meta | R-HERO | 75.81 | 3.12 | 38.09 | 122516 | 0.09 | 6.16 |
| Hifiasm-meta | MLRC | 73.40 | 5.65 | 24.14 | 143247 | 0.00 | 7.84 |
| Hifiasm-meta | F-HERO | 72.24 | 3.96 | 20.79 | 132107 | 0.02 | 7.84 |
| Hifiasm-meta | LoRDEC | 70.17 | 7.14 | 24.42 | 115314 | 0.00 | 7.59 |
| Hifiasm-meta | L-HERO | 71.34 | 3.20 | 21.05 | 118102 | 0.03 | 6.24 |
| Bmock12 PacBio | |||||||
| Hifiasm-meta | Ratatosk | 58.76 | 28.69 | 56.05 | 25507 | 0.36 | 5.40 |
| Hifiasm-meta | R-HERO | 61.97 | 7.80 | 35.78 | 28983 | 0.05 | 4.80 |
| Hifiasm-meta | FMLRC | 67.90 | 5.84 | 20.34 | 33664 | 0.00 | 5.20 |
| Hifiasm-meta | F-HERO | 67.94 | 4.53 | 17.71 | 31602 | 0.01 | 5.60 |
| Hifiasm-meta | LoRDEC | 56.53 | 7.08 | 22.48 | 29667 | 0.00 | 6.02 |
| Hifiasm-meta | L-HERO | 62.42 | 3.56 | 21.58 | 30746 | 0.02 | 5.10 |
| NWC ONT | |||||||
| Hifiasm-meta | Ratatosk | 66.86 | 155.25 | 264.14 | 35297 | 9.25 | 31.69 |
| Hifiasm-meta | R-HERO | 73.99 | 84.48 | 270.01 | 39254 | 5.68 | 29.93 |
| Hifiasm-meta | FMLRC | 70.68 | 52.21 | 105.07 | 46395 | 0.00 | 30.74 |
| Hifiasm-meta | F-HERO | 73.17 | 32.38 | 128.81 | 51599 | 0.00 | 29.17 |
| Hifiasm-meta | LoRDEC | 32.56 | 86.05 | 402.98 | - | 0.00 | 35.63 |
| Hifiasm-meta | L-HERO | 50.23 | 43.10 | 258.81 | 6813 | 0.00 | 42.26 |
| NWC PacBio | |||||||
| Hifiasm-meta | Ratatosk | 54.19 | 141.16 | 450.63 | 25309 | 1.83 | 8.12 |
| Hifiasm-meta | R-HERO | 58.39 | 44.81 | 136.94 | 27327 | 1.01 | 5.03 |
| Hifiasm-meta | FMLRC | 55.88 | 46.17 | 153.2 | 28732 | 0.00 | 6.86 |
| Hifiasm-meta | F-HERO | 59.54 | 31.15 | 180.53 | 29612 | 0.00 | 6.26 |
| Hifiasm-meta | LoRDEC | 38.38 | 48.11 | 327.45 | 9535 | 0.00 | 16.13 |
| Hifiasm-meta | L-HERO | 45.94 | 41.72 | 588.42 | 19398 | 0.00 | 10.55 |
Boldface is meant to indicate the best performing tool in the respective category