Table 1.
Benchmark results for correcting simulated PacBio CLR reads. 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
| Correction | Indels/100 kbp | Mismatches/100 kbp | GF (%) | N/100 kbp | MC (%) |
|---|---|---|---|---|---|
| 3 Salmonella strains | |||||
| PacBio CLR reads (10X) | 6053.09 | 1564.71 | 99.96 | 0.00 | 0.00 |
| Ratatosk | 110.75 | 128.23 | 99.96 | 6.53 | 0.29 |
| R-HERO | 11.77 | 93.90 | 99.96 | 0.76 | 0.20 |
| FMLRC | 83.26 | 215.29 | 99.96 | 0.00 | 0.11 |
| F-HERO | 17.47 | 194.45 | 99.96 | 0.00 | 0.13 |
| LoRDEC | 59.00 | 197.74 | 99.95 | 0.00 | 0.00 |
| L-HERO | 11.58 | 181.06 | 99.96 | 0.00 | 0.01 |
| 20 bacteria strains | |||||
| PacBio CLR reads (10X) | 6123.04 | 1594.90 | 99.32 | 0.14 | 0.00 |
| Ratatosk | 402.71 | 171.31 | 99.02 | 3.34 | 0.06 |
| R-HERO | 26.54 | 103.51 | 98.47 | 0.43 | 0.13 |
| FMLRC | 314.82 | 325.05 | 96.09 | 0.02 | 0.99 |
| F-HERO | 72.40 | 275.34 | 95.46 | 0.00 | 1.11 |
| LoRDEC | 229.92 | 267.60 | 97.15 | 0.00 | 0.015 |
| L-HERO | 34.25 | 230.43 | 96.51 | 0.00 | 0.182 |
| 100 bacteria strains | |||||
| PacBio CLR reads (10X) | 6194.76 | 1644.52 | 98.07 | 0.00 | 0.001 |
| Ratatosk | 523.07 | 267.42 | 99.45 | 6.30 | 0.29 |
| R-HERO | 46.10 | 250.16 | 98.42 | 1.04 | 0.85 |
| FMLRC | 413.23 | 561.24 | 94.27 | 0.00 | 2.31 |
| F-HERO | 97.84 | 511.03 | 94.79 | 0.00 | 3.47 |
| LoRDEC | 392.21 | 517.00 | 96.36 | 0.00 | 0.14 |
| L-HERO | 63.56 | 470.06 | 96.07 | 0.00 | 1.10 |
Boldface is meant to indicate the best performing tool in the respective category