Table 1 Basecalling comparison: run-times, read accuracy and overall assembly accuracy
From: MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction
| Â | Guppy3.4.3_hac | Guppy3.4.3_fast | Guppy3.4.3_hac_modbases | Guppy3.6.1_hac | Guppy3.6.1_hac_ modbases |
|---|---|---|---|---|---|
Basecalling comparison: | |||||
 Run time (ms) | 49,707,952 | 176,906,144 | 57,479,661 | 57,977,178 | 46,296,565 |
 Run time (h) | 13.81 | 49.14 | 15.96 | 16.10 | 12.86 |
 GPU/CPU | GPU | CPU | GPU | GPU | GPU |
 Num callers | 4 | 16 | 8 | 8 | 8 |
 Average read percent identity | 91.0 | 88.9 | 90.6 | 93.7 | 91.0 |
 Mean read quality | 11.4 | 10.4 | 11.3 | 13.3 | 11.4 |
 Number of binned reads (qcat) | 240,766 | 233,802 | 238,847 | 244,830 | 240,156 |
Final assembly comparison: | |||||
 Assembly nucleotide identity (%) | 99.99 | 99.99 | 99.99 | 99.99 | 99.99 |
 Number of SNP (DNAdiff) | 23 | 35 | 3 | 4 | 5 |
 Number of indels (DNAdiff) | 45 | 39 | 31 | 25 | 27 |
 Assembly quality score (Pomoxis) | 48.10 | 48.08 | 50.99 | 52.27 | 51.83 |
 Mismatches per 100 kb (QUAST) | 0.44 | 0.67 | 0.06 | 0.08 | 0.10 |
 Indels per 100 kb (QUAST) | 0.88 | 0.76 | 0.63 | 0.50 | 0.53 |