Table 2 Summary of the software comparison between varVAMP, Olivar and PrimalScheme
From: varVAMP: degenerate primer design for tiled full genome sequencing and qPCR
SARS-CoV-2 | BoDV-1 | HAV | HEV cluster 2 | HEV cluster 4 | PV | ratHEV | ||
|---|---|---|---|---|---|---|---|---|
varVAMP | Running time | 1 min 9 s | 16 s | 12 s | 22 s | 10 s | 11 s | 9 s |
Number of amplicons | 55 | 27 | 7 | 7 | 6 | 7 | 6 | |
% alignment coverage | 100 | 99 | 96 | 99 | 99 | 100 | 97 | |
Mean mismatches per primer | 0.002 | 0.17 | 0.15 | 0.21 | 0.20 | 0.13 | 0.43 | |
Olivar | Running time | 14 min 54 s | 2 min 55 s | 38 s | 37 s | 39 s | 52 s | 28 s |
Number of amplicons | 61 | 28 | 5 | 7 | 8 | 10 | 5 | |
% alignment coverage | 99 | 95 | 79 | 94 | 92 | 99 | 81 | |
Mean mismatches per primer | 0.001 | 0.44 | 0.88 | 1.03 | 1.09 | 1.63 | 2.11 | |
Primalscheme (alignment) | Running time | 7 min 32 s | 23 min 52 s | 17 h 11 min 33 s | 8 h 8 min 4 s | 50 h 25 min 56 s | 5 h 37 min 56 s | 48 s |
Number of amplicons | 49 | 25 | 6 | 8 | 8 | 8 | 6 | |
% alignment coverage | 100 | 88 | 79 | 99 | 97 | 95 | 91 | |
Mean mismatches per primer | 0.027 | 0.29 | 0.78 | 1.04 | 1.19 | 1.65 | 4.17 | |
Primalscheme (consensus) | Running time | 8 s | 5 s | 6 s | 4 s | 4 s | 4 s | 4 s |
Number of amplicons | 49 | 28 | 8 | 8 | 8 | 8 | 6 | |
% alignment coverage | 100 | 99 | 93 | 96 | 97 | 96 | 92 | |
Mean mismatches per primer | 0.027 | 0.73 | 1.63 | 1.48 | 1.63 | 2.60 | 3.04 |
