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Table 4 The classification of denoised sequences from the nine test data sets

From: Removing Noise From Pyrosequenced Amplicons

Name Unique Good Bimera Trimera Quadramera Unclassified
Divergent
AmpliconNoise 79 56(70.9%) 21(26.6%) 1(1.3%) 0 (0.0%) 1(1.3%)
SLP 1% 305 210 (68.9%) 23 (7.5%) 1 (0.3%) 0 (0.0%) 71(23.3%)
SLP 2% 60 29 (48.3%) 22 (36.7%) 0 (0.0%) 0 (0.0%) 9(15.0%)
DeNoiser 37 28 (75.7%) 7 (18.9%) 1 (2.7%) 0 (0.0) 1(2.7%)
Artificial
AmpliconNoise 118 94(79.7%) 21(17.8%) 0 (0.0%) 0 (0.0%) 3(2.5%)
SLP 1% 230 168 (73.0%) 21 (9.1%) 0 (0.0%) 0 (0.0%) 41(17.9%)
SLP 2% 62 36 (58.1%) 20 (32.3%) 0 (0.0%) 0 (0.0%) 6(9.7%)
DeNoiser 59 46 (78.0%) 8 (13.6%) 0 (0.0%) 0 (0.0%) 5(8.5%)
Even1
AmpliconNoise 2341 89 (3.8%) 1847 (78.9%) 244 (10.4%) 4 (0.2%) 157(6.7%)
SLP 1% 2205 108 (4.9%) 1631 (74.0%) 253 (11.5%) 4 (0.2%) 209(9.5%)
SLP 2% 894 38 (4.3%) 638 (71.4%) 142 (15.9%) 4 (0.4%) 72(8.1%)
DeNoiser 289 63 (21.8%) 161 (55.7%) 36 (12.5%) 3 (1.0%) 26(9.0%)
Even2
AmpliconNoise 2082 90 (4.3%) 1651 (79.3%) 227 (10.9%) 4 (0.2%) 110(5.3%)
SLP 1% 1958 97 (5.0%) 1448 (74.0%) 235 (12.0%) 4 (0.2%) 174(8.9%)
SLP 2% 789 44 (5.6%) 553 (70.1%) 134 (17.0%) 4 (0.5%) 54(6.8%)
DeNoiser 285 64 (22.5%) 171 (60.0%) 22 (7.7%) 4 (1.4%) 24(8.4%)
Even3
AmpliconNoise 2210 91 (4.1%) 1781 (80.6%) 188 (8.5%) 3 (0.1%) 147(6.7%)
SLP 1% 2164 117 (5.4%) 1635 (75.6%) 194 (9.0%) 3 (0.1%) 215(9.9%)
SLP 2% 874 40 (4.6%) 649 (74.3%) 105 (12.0%) 1 (0.1%) 79(9.0%)
Denoiser 287 64 (22.3%) 170 (59.2%) 24 (8.4%) 0 (0.0%) 29(10.1%)
Uneven1
AmpliconNoise 1124 94 (8.4%) 816 (72.6%) 81 (7.2%) 1 (0.1%) 132(11.7%)
SLP 1% 1040 90 (8.7%) 682 (65.6%) 88 (8.5%) 2 (0.2%) 178(17.1%)
SLP 2% 439 51 (11.6%) 278 (63.3%) 49 (11.2%) 1 (0.2%) 60(13.7%)
Denoiser 212 61 (28.8%) 111 (52.4%) 9 (4.2%) 0 (0.0%) 31(14.6%)
Uneven2
AmpliconNoise 859 77 (9.0%) 669 (77.9%) 71 (8.3%) 2 (0.2%) 40(4.7%)
SLP 1% 814 81 (10.0%) 570 (70.0%) 77 (9.5%) 2 (0.2%) 84(10.3%)
SLP 2% 330 36 (10.9%) 226 (68.5%) 36 (10.9%) 2 (0.6%) 30(9.1%)
Denoiser 154 49 (31.8%) 87 (56.5%) 9 (5.8%) 1 (0.6%) 8(5.2%)
Uneven3
AmpliconNoise 1053 75 (7.1%) 843 (80.1%) 82 (7.8%) 0 (0.0%) 53(5.0%)
SLP 1% 1031 89 (8.6%) 745 (72.3%) 92 (8.9%) 0 (0.0%) 105(10.2%)
SLP 2% 399 45 (11.3%) 259 (64.9%) 49 (12.3%) 0 (0.0%) 46(11.5%)
Denoiser 202 55 (27.2%) 124 (61.4%) 7 (3.5%) 0 (0.0%) 16(7.9%)
Titanium
AmpliconNoise - σ s = 0.1 163 76 (46.6%) 77 (47.2%) 1 (0.6%) 0 (0.0%) 9(5.5%)
AmpliconNoise - σ s = 0.04 304 91 (29.9%) 174 (57.2%) 2 (0.7%) 0 (0.0%) 37(12.2%)
SLP 1% 765 520 (68.0%) 157 (20.5%) 1 (0.1%) 0 (0.0%) 87(11.4%)
SLP 2% 182 72 (39.6%) 92 (50.5%) 1(0.5%) 0 (0.0%) 17(9.3%)
DeNoiser 151 14 (9.3%) 70 (46.4%) 6(4.0%) 0 (0.0%) 61(40.4%)
  1. The number of unique denoised sequences classified into the five categories, 'Good', 'Bimera', 'Trimera', 'Quadramera' and 'Unclassified', as defined in the text are given together with percentages of the total in parentheses.