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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

  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