Table 3 Results on assembly after correction by different correction protocols of reads from 4 different real datasets. 1st column: genome assembly program; Canu was used for raw reads, while HiCanu was used for corrected reads (because their error profiles resemble those of PacBio HiFI reads). 2nd column: Error correction protocol. 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. NGA50 is the length of the longest contig such that the alignments of that and all longer contigs span at least 50% of the reference sequence. N/100 kbp denotes the average number of uncalled bases (Ns) per 100,000 bases in the read. MC = fraction of misassembled contigs
From: Hybrid-hybrid correction of errors in long reads with HERO
Assemblers | GF (%) | Indels/100 kbp | Mismatches/100 kbp | NGA50 | N/100 kbp | MC (%) | |
|---|---|---|---|---|---|---|---|
Bmock12 ONT | |||||||
Canu | ONT raw reads | 57.13 | 504.95 | 140.75 | 78498 | 0.00 | 9.04 |
HiCanu | Ratatosk | 61.56 | 2.99 | 83.12 | 137201 | 0.22 | 4.04 |
HiCanu | R-HERO | 63.92 | 1.27 | 34.30 | 198551 | 0.07 | 2.70 |
HiCanu | FMLRC | 60.64 | 1.10 | 8.76 | 136705 | 0.00 | 4.48 |
HiCanu | F-HERO | 60.84 | 0.82 | 6.90 | 148570 | 0.03 | 4.23 |
HiCanu | LoRDEC | 56.48 | 1.43 | 9.92 | 90070 | 0.00 | 4.28 |
HiCanu | L-HERO | 60.50 | 1.14 | 16.48 | 125982 | 0.03 | 4.74 |
Bmock12 PacBio | |||||||
Canu | PacBio raw reads | 50.01 | 174.71 | 63.79 | 6025 | 0.00 | 3.72 |
HiCanu | Ratatosk | 59.25 | 3.88 | 66.22 | 31170 | 0.46 | 2.61 |
HiCanu | R-HERO | 61.48 | 1.85 | 38.50 | 42481 | 0.06 | 4.60 |
HiCanu | FMLRC | 62.54 | 2.02 | 19.50 | 65939 | 0.00 | 2.40 |
HiCanu | F-HERO | 62.83 | 1.77 | 19.28 | 61786 | 0.03 | 2.45 |
HiCanu | LoRDEC | 55.47 | 1.67 | 23.59 | 23307 | 0.00 | 2.96 |
HiCanu | L-HERO | 60.27 | 1.72 | 35.59 | 44240 | 0.01 | 6.51 |
NWC ONT | |||||||
Canu | ONT raw reads | - | - | - | - | - | - |
HiCanu | Ratatosk | 75.74 | 88.44 | 173.91 | 47297 | 5.39 | 42.06 |
HiCanu | R-HERO | 78.72 | 48.09 | 179.33 | 52662 | 3.05 | 53.51 |
HiCanu | FMLRC | 84.95 | 66.68 | 180.80 | 61515 | 0.00 | 50.25 |
HiCanu | F-HERO | 89.12 | 37.92 | 160.21 | 84587 | 0.00 | 50.48 |
HiCanu | LoRDEC | 36.71 | 42.98 | 185.76 | - | 0.00 | 21.54 |
HiCanu | L-HERO | 61.66 | 27.54 | 141.29 | 37960 | 0.00 | 31.11 |
NWC PacBio | |||||||
Canu | PacBio raw reads | 44.27 | 62.25 | 33.51 | - | 0.00 | 36.51 |
HiCanu | Ratatosk | 49.66 | 18.72 | 59.16 | 28052 | 2.15 | 6.32 |
HiCanu | R-HERO | 53.38 | 11.10 | 57.32 | 29365 | 1.97 | 9.52 |
HiCanu | FMLRC | 51.28 | 20.84 | 32.52 | 29528 | 0.00 | 6.12 |
HiCanu | F-HERO | 53.39 | 15.98 | 44.49 | 33130 | 0.00 | 11.10 |
HiCanu | LoRDEC | 50.34 | 8.27 | 56.65 | 26773 | 0.00 | 5.81 |
HiCanu | L-HERO | 51.04 | 6.43 | 54.91 | 27546 | 0.00 | 5.98 |