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 |
 | Bonito_CTC | 96.87 | 91.44 | 3,676,821 | 38.9 | 3,676,821 | 210,496 | 5.72 | 12.45 |
 | SACall | 96.68 | 89.42 | 3,699,232 | 38.7 | 3,699,232 | 247,997 | 6.7 | 12.1 |
 | Dorado-fast | 96.37 | 88.72 | 3,839,847 | 39.09 | 3,839,847 | 245,016 | 6.38 | 12.03 |
 | RUBICALL | 96.87 | 91.51 | 3,694,086 | 38.82 | 3,694,086 | 208,748 | 5.65 | 15.42 |
 | 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 |
 | SACall | 90.11 | 88.45 | 2,032,994 | 38.22 | 1,880,730 | 134,702 | 6.63 | 13.15 |
 | Dorado-fast | 89.42 | 88.97 | 2,110,860 | 39.49 | 2,110,860 | 129,503 | 6.14 | 12.38 |
 | RUBICALL | 96.87 | 90.54 | 1,966,781 | 38.92 | 1,966,781 | 119,777 | 6.09 | 15.37 |
 | 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 |
 | SACall | 93.97 | 88.08 | 4,874,880 | 56.87 | 4,874,880 | 379,028 | 7.78 | 10.8 |
 | Dorado-fast | 93.00 | 87.69 | 5,063,562 | 56.8 | 5,063,562 | 348,572 | 6.88 | 10.64 |
 | RUBICALL | 94.51 | 90.30 | 4,924,240 | 56.85 | 4,924,240 | 314,651 | 6.39 | 11.27 |
 | 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 |
 | SACall | 92.93 | 88.60 | 5,149,039 | 56.72 | 5,149,039 | 369,388 | 7.17 | 11.08 |
 | Dorado-fast | 90.21 | 88.20 | 5,737,059 | 56.44 | 5,401,717 | 342,141 | 5.96 | 10.98 |
 | RUBICALL | 93.12 | 90.60 | 5,146,050 | 56.72 | 5,146,050 | 312,448 | 6.07 | 11.42 |
 | 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 |
 | SACall | 93.58 | 88.19 | 5,034,408 | 56.79 | 5,034,408 | 372,380 | 7.4 | 11.16 |
 | Dorado-fast | 90.28 | 87.67 | 5,442,186 | 56.72 | 5,261,731 | 349,387 | 6.42 | 11.03 |
 | RUBICALL | 93.07 | 89.89 | 5,023,639 | 56.75 | 4,932,626 | 357,769 | 7.12 | 11.25 |
 | 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 |
 | SACall | 93.66 | 88.58 | 4,978,307 | 57.06 | 4,978,307 | 360,950 | 7.25 | 11.56 |
 | Dorado-fast | 92.27 | 88.12 | 5,195,594 | 57.01 | 5,195,594 | 355,728 | 6.85 | 11.56 |
 | RUBICALL | 94.36 | 90.43 | 4,940,813 | 57.18 | 4,940,813 | 316,019 | 6.4 | 11.83 |
 | 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 |
 | SACall | 94.29 | 89.36 | 5,366,913 | 58.57 | 5,366,913 | 358,954 | 6.69 | 12.27 |
 | Dorado-fast | 96.51 | 88.87 | 5,758,989 | 58.29 | 5,282,474 | 348,968 | 6.06 | 12.5 |
 | RUBICALL | 96.76 | 91.59 | 5,597,251 | 58.52 | 5,346,640 | 294,643 | 5.26 | 13.01 |
 | 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 |
 | SACall | 95.66 | 91.25 | 2,837,503 | 32.91 | 2,798,079 | 165,200 | 5.82 | 11.57 |
 | Dorado-fast | 96.70 | 91.16 | 2,927,882 | 33.52 | 2,752,169 | 152,216 | 5.2 | 11.64 |
 | RUBICALL | 97.03 | 93.36 | 2,860,885 | 33.24 | 2,821,276 | 124,795 | 4.36 | 12.59 |
 | 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 |
 | SACall | 95.28 | 88.50 | 4,672,540 | 64.98 | 4,672,540 | 339,853 | 7.27 | 11.11 |
 | Dorado-fast | 92.99 | 87.70 | 4,854,007 | 63.99 | 4,854,007 | 337,105 | 6.94 | 11.01 |
 | RUBICALL | 95.46 | 90.49 | 4,693,744 | 65.03 | 4,693,744 | 289,073 | 6.16 | 11.63 |
 | 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 |
 | Bonito_CTC | 0.430 | 95.06 | 134,732,516 | 40.86 | 371,590 | 384,243 | 0.29 | 18.58 |
 | SACall | NA | NA | 63,025,520 | 39.87 | 320,873 | NA | NA | NA |
 | Dorado-fast | 0.001 | 93.15 | 121,146,376 | 39.8 | 361,677 | 926 | 0 | 17.46 |
 | RUBICALL | 0.125 | 94.50 | 140,928,248 | 40.99 | 393,950 | 100,256 | 0.1 | 17.81 |
 | Reference | 100 | 100 | 2,947,743,500 | 40.79 | 2,947,743,500 | 0 | 0 | - |