Table 1 Assembly quality comparison of the evaluated basecallers for different species. We measure assembly accuracy in terms of genome fraction (Genome Fraction (%)) and average identity (Average Identity (%)). Genome fraction is the portion of the Reference genome that can align to a given assembly, while average identity is the average of the identity of assemblies when compared to their respective Reference genomes. We measure statistics related to the contiguity and completeness of the assemblies in terms of the overall assembly length (Assembly Length), Average GC content (Average GC (%)) (i.e., the ratio of G and C bases in an assembly), NG50 statistics (NG50) (i.e., shortest contig at the half of the overall Reference genome length), total number of indels in all aligned bases in the assembly (Total Indels), the ratio of indels to assembly length (Indel Ratio (%)), and the reliability of basepairs using the quality value (Quality Value). NA indicates that the generated assemblies were unalignable to the reference genome
From: RUBICON: a framework for designing efficient deep learning-based genomic basecallers
Dataset | Basecaller | Genome fraction (%) | Average identity (%) | Assembly length | Average GC (%) | NG50 | Total indels | Indel ratio (%) | Quality value (QV) |
|---|---|---|---|---|---|---|---|---|---|
Acinetobacter | Causalcall | 92.45 | 86.18 | 3,826,077 | 42.23 | 3,826,077 | 270,228 | 7.06 | 11.99 |
pittii 16-377-0801 | Bonito_CRF-fast | 96.64 | 89.29 | 3,628,317 | 38.82 | 3,628,317 | 242,373 | 6.68 | 12.03 |
| Â | Bonito_CTC | 96.87 | 91.44 | 3,676,821 | 38.9 | 3,676,821 | 210,496 | 5.72 | 12.45 |
| Â | SACall | 96.68 | 89.42 | 3,699,232 | 38.7 | 3,699,232 | 247,997 | 6.7 | 12.1 |
| Â | Dorado-fast | 96.37 | 88.72 | 3,839,847 | 39.09 | 3,839,847 | 245,016 | 6.38 | 12.03 |
| Â | RUBICALL | 96.87 | 91.51 | 3,694,086 | 38.82 | 3,694,086 | 208,748 | 5.65 | 15.42 |
| Â | Reference | 100 | 100 | 3,814,719 | 38.78 | 3,814,719 | 0 | 0 | - |
Haemophilus | Causalcall | 0.00 | 0.00 | 0 | 0 | 0 | 0 | 0 | NA |
haemolyticus | Bonito_CRF-fast | 88.76 | 91.51 | 2,046,024 | 37.98 | 2,046,024 | 128,481 | 6.28 | 12.25 |
M1C132_1 | Bonito_CTC | 96.87 | 90.70 | 1,957,480 | 38.87 | 1,957,480 | 118,253 | 6.04 | 15.34 |
| Â | SACall | 90.11 | 88.45 | 2,032,994 | 38.22 | 1,880,730 | 134,702 | 6.63 | 13.15 |
| Â | Dorado-fast | 89.42 | 88.97 | 2,110,860 | 39.49 | 2,110,860 | 129,503 | 6.14 | 12.38 |
| Â | RUBICALL | 96.87 | 90.54 | 1,966,781 | 38.92 | 1,966,781 | 119,777 | 6.09 | 15.37 |
| Â | Reference | 100 | 100 | 2,042,591 | 38.46 | 2,042,591 | 0 | 0 | - |
Klebsiella | Causalcall | 92.45 | 87.35 | 4,959,127 | 56.9 | 4,959,127 | 353,550 | 7.13 | 10.54 |
pneumoniae | Bonito_CRF-fast | 92.69 | 87.53 | 4,761,297 | 57.19 | 4,761,297 | 347,299 | 7.29 | 10.56 |
INF032 | Bonito_CTC | 94.50 | 90.20 | 4,897,352 | 56.65 | 4,897,352 | 317,428 | 6.48 | 11.26 |
| Â | SACall | 93.97 | 88.08 | 4,874,880 | 56.87 | 4,874,880 | 379,028 | 7.78 | 10.8 |
| Â | Dorado-fast | 93.00 | 87.69 | 5,063,562 | 56.8 | 5,063,562 | 348,572 | 6.88 | 10.64 |
| Â | RUBICALL | 94.51 | 90.30 | 4,924,240 | 56.85 | 4,924,240 | 314,651 | 6.39 | 11.27 |
| Â | Reference | 100 | 100 | 5,111,537 | 57.63 | 5,111,537 | 0 | 0 | - |
Klebsiella | Causalcall | 91.44 | 87.36 | 5,288,166 | 56.94 | 5,288,166 | 374,162 | 7.08 | 10.84 |
pneumoniae | Bonito_CRF-fast | 92.08 | 88.49 | 5,052,889 | 56.8 | 5,052,889 | 357,354 | 7.07 | 10.93 |
INF042 | Bonito_CTC | 93.12 | 90.49 | 5,111,083 | 56.61 | 5,111,083 | 317,075 | 6.2 | 11.40 |
| Â | SACall | 92.93 | 88.60 | 5,149,039 | 56.72 | 5,149,039 | 369,388 | 7.17 | 11.08 |
| Â | Dorado-fast | 90.21 | 88.20 | 5,737,059 | 56.44 | 5,401,717 | 342,141 | 5.96 | 10.98 |
| Â | RUBICALL | 93.12 | 90.60 | 5,146,050 | 56.72 | 5,146,050 | 312,448 | 6.07 | 11.42 |
| Â | Reference | 100 | 100 | 5,337,491 | 57.41 | 5,337,491 | 0 | 0 | - |
Klebsiella | Causalcall | 91.58 | 86.97 | 5,175,311 | 57.09 | 5,175,311 | 363,807 | 7.03 | 10.88 |
pneumoniae | Bonito_CRF-fast | 90.24 | 88.00 | 4,932,626 | 56.71 | 4,932,626 | 357,769 | 7.25 | 10.86 |
KSB2_1B | Bonito_CTC | 93.07 | 90.11 | 5,003,377 | 56.69 | 5,003,377 | 320,519 | 6.41 | 11.41 |
| Â | SACall | 93.58 | 88.19 | 5,034,408 | 56.79 | 5,034,408 | 372,380 | 7.4 | 11.16 |
| Â | Dorado-fast | 90.28 | 87.67 | 5,442,186 | 56.72 | 5,261,731 | 349,387 | 6.42 | 11.03 |
| Â | RUBICALL | 93.07 | 89.89 | 5,023,639 | 56.75 | 4,932,626 | 357,769 | 7.12 | 11.25 |
| Â | Reference | 100 | 100 | 5,228,889 | 57.59 | 5,228,889 | 0 | 0 | - |
Klebsiella | Causalcall | 89.08 | 86.01 | 5,158,874 | 56.78 | 5,158,874 | 389,676 | 7.55 | 11.75 |
pneumoniae | Bonito_CRF-fast | 92.17 | 89.34 | 4,942,833 | 57.01 | 4,942,833 | 355,690 | 7.2 | 11.47 |
NUH29 | Bonito_CTC | 94.36 | 90.26 | 4,918,147 | 57.04 | 4,918,147 | 324,406 | 6.6 | 11.92 |
| Â | SACall | 93.66 | 88.58 | 4,978,307 | 57.06 | 4,978,307 | 360,950 | 7.25 | 11.56 |
| Â | Dorado-fast | 92.27 | 88.12 | 5,195,594 | 57.01 | 5,195,594 | 355,728 | 6.85 | 11.56 |
| Â | RUBICALL | 94.36 | 90.43 | 4,940,813 | 57.18 | 4,940,813 | 316,019 | 6.4 | 11.83 |
| Â | Reference | 100 | 100 | 5,134,281 | 57.61 | 5,134,281 | 0 | 0 | - |
Serratia | Causalcall | 89.91 | 86.23 | 5,532,953 | 57.86 | 5,422,052 | 401,545 | 7.26 | 13.39 |
marcescens | Bonito_CRF-fast | 96.06 | 89.56 | 5,479,812 | 58.85 | 5,282,474 | 345,351 | 6.3 | 12.66 |
17-147-1671 | Bonito_CTC | 96.76 | 91.38 | 5,534,329 | 58.41 | 5,316,651 | 298,982 | 5.4 | 13 |
| Â | SACall | 94.29 | 89.36 | 5,366,913 | 58.57 | 5,366,913 | 358,954 | 6.69 | 12.27 |
| Â | Dorado-fast | 96.51 | 88.87 | 5,758,989 | 58.29 | 5,282,474 | 348,968 | 6.06 | 12.5 |
| Â | RUBICALL | 96.76 | 91.59 | 5,597,251 | 58.52 | 5,346,640 | 294,643 | 5.26 | 13.01 |
| Â | Reference | 100 | 100 | 5,517,578 | 59.13 | 5,517,578 | 0 | 0 | - |
Staphylococcus | Causalcall | 94.35 | 87.29 | 2,849,123 | 36.59 | 2,810,038 | 191,730 | 6.73 | 10.8 |
aureus | Bonito_CRF-fast | 96.27 | 91.49 | 2,790,895 | 33.05 | 2,752,169 | 149,623 | 5.36 | 11.59 |
CAS38_02 | Bonito_CTC | 97.03 | 93.57 | 2,858,986 | 32.86 | 2,819,356 | 123,542 | 4.32 | 12.82 |
| Â | SACall | 95.66 | 91.25 | 2,837,503 | 32.91 | 2,798,079 | 165,200 | 5.82 | 11.57 |
| Â | Dorado-fast | 96.70 | 91.16 | 2,927,882 | 33.52 | 2,752,169 | 152,216 | 5.2 | 11.64 |
| Â | RUBICALL | 97.03 | 93.36 | 2,860,885 | 33.24 | 2,821,276 | 124,795 | 4.36 | 12.59 |
| Â | Reference | 100 | 100 | 2,902,076 | 32.82 | 2,902,076 | 0 | 0 | - |
Stenotrophomonas | Causalcall | 94.85 | 85.73 | 4,823,177 | 63.66 | 4,823,177 | 366,228 | 7.59 | 11.01 |
maltophilia | Bonito_CRF-fast | 94.60 | 89.74 | 4,596,898 | 65.5 | 4,596,898 | 337,040 | 7.33 | 11.10 |
17_G_0092_Kos | Bonito_CTC | 95.42 | 90.14 | 4,664,226 | 64.82 | 4,664,226 | 298,711 | 6.4 | 11.51 |
| Â | SACall | 95.28 | 88.50 | 4,672,540 | 64.98 | 4,672,540 | 339,853 | 7.27 | 11.11 |
| Â | Dorado-fast | 92.99 | 87.70 | 4,854,007 | 63.99 | 4,854,007 | 337,105 | 6.94 | 11.01 |
| Â | RUBICALL | 95.46 | 90.49 | 4,693,744 | 65.03 | 4,693,744 | 289,073 | 6.16 | 11.63 |
| Â | Reference | 100 | 100 | 4,802,733 | 66.28 | 4,802,733 | 0 | 0 | - |
Human | Causalcall | NA | NA | 130,962 | 42.95 | 13,522 | NA | NA | NA |
HG002 | Bonito_CRF-fast | 0.002 | 92.36 | 119,570,537 | 40.34 | 368,848 | 2860 | 0 | 18.87 |
| Â | Bonito_CTC | 0.430 | 95.06 | 134,732,516 | 40.86 | 371,590 | 384,243 | 0.29 | 18.58 |
| Â | SACall | NA | NA | 63,025,520 | 39.87 | 320,873 | NA | NA | NA |
| Â | Dorado-fast | 0.001 | 93.15 | 121,146,376 | 39.8 | 361,677 | 926 | 0 | 17.46 |
| Â | RUBICALL | 0.125 | 94.50 | 140,928,248 | 40.99 | 393,950 | 100,256 | 0.1 | 17.81 |
| Â | Reference | 100 | 100 | 2,947,743,500 | 40.79 | 2,947,743,500 | 0 | 0 | - |