Additional file 1. Supplementary Table S1: Descriptive and diversity parameters of each simulated dataset. Page 2. Supplementary Table S2: Sensitivity (in %) and precision (in %) in simulated datasets generated by MetaSim. Page 3. Supplementary Table S3: List of genomes and number of reads used in each simulated dataset. Page 4. Supplementary Table S4: List of genomes used to build BLAST database and to train Phymm and NBC. Page 40. Additional data files:
simulated_files.zip: simulated and synthetic sequences generated using our scripts in FASTA format, and their keys simulated_metasim.zip: simulated sequences generated using metasim in FASTA format simulated_imess.zip: simulated sequences generated using iMESS in FASTA format, and their keys
Supplementary Table S1: Descriptive and diversity parameters of each simulated dataset.
Simulated dataset
| Analyzed bp
| Number of reads
| Genomes used
| Number of reads from most abundant genome
| Size of read
| H’
| Average
| Standard deviation
| Maximum
| Minimum
|
| All genomes
| 19513675
| 60000
| 42
| 2918
| 325.2
| 100.71
| 499
| 151
| 3.52
| All genomes (dominant)
| 19451450
| 60000
| 4
| 40523
| 324.2
| 100.57
| 499
| 151
| 0.89
| Bacterial genomes
| 19784302
| 59170
| 42
| 2981
| 334.4
| 116.36
| 987
| 151
| 3.54
| Bacterial genomes (dominant)
| 19532051
| 60000
| 2
| 32460
| 325.5
| 100.85
| 151
| 499
| 0.69
| MetaSim1
| 16052049
| 60000
| 1261
| 219
| 267.5
| 19.1
| 394
| 202
| 6.70
| MetaSim2
| 16055024
| 60000
| 1265
| 223
| 267.6
| 19.23
| 413
| 193
| 6.71
| MetaSim3
| 16354917
| 60000
| 16
| 8640
| 272.6
| 16.55
| 368
| 194
| 2.28
| MetaSim4
| 16282072
| 60000
| 10
| 10548
| 271.4
| 16.22
| 359
| 197
| 1.99
| iMESS1
| 12526912
| 49560
| 125
| 2414
| 252.8
| 2.40
| 264
| 243
| 4.61
| iMESS2
| 12464015
| 49308
| 135
| 2348
| 252.8
| 2.40
| 264
| 243
| 4.60
|
Supplementary Table S2: Sensitivity (in %) and precision (in %) in simulated datasets generated by MetaSim.
| Sensitivity
| Precision
|
| Phymm
| Bayesian
| LCA
| Combined
| Phymm
| Bayesian
| LCA
| Combined
| Phylum
|
|
|
|
|
|
|
|
| MetaSim 1
| 62.41
| 77.73
| 95.55
| 85.45
| 73.78
| 84.11
| 100
| 96.58
| MetaSim 2
| 62.27
| 77.88
| 95.5
| 85.56
| 73.71
| 84.14
| 100
| 96.51
| MetaSim 3
| 65.39
| 68.73
| 94
| 84.04
| 79.85
| 85.71
| 100
| 84.04
| MetaSim 4
| 65.98
| 74.09
| 99.68
| 88.27
| 80.73
| 87.55
| 100
| 88.28
| iMESS1
| 53.48
| 66.87
| 77.51
| 71.72
| 62.76
| 71.79
| 82.57
| 80.89
| iMESS2
| 56.43
| 68.05
| 79.57
| 73.03
| 66.01
| 72.95
| 84.34
| 81.84
| Class
|
|
|
|
|
|
|
|
| MetaSim 1
| 42.63
| 57.49
| 73.41
| 62.85
| 52.84
| 63.91
| 76.69
| 77.42
| MetaSim 2
| 42.64
| 57.82
| 73.43
| 62.95
| 52.92
| 64.12
| 76.7
| 77.47
| MetaSim 3
| 62.42
| 66.94
| 93.98
| 82.22
| 79.47
| 84.15
| 100
| 82.23
| MetaSim 4
| 62.14
| 72.03
| 99.67
| 86
| 79.52
| 85.75
| 100
| 86
| iMESS1
| 37.43
| 53.09
| 65.78
| 56.46
| 45.57
| 58.49
| 69.77
| 69.7
| iMESS2
| 40.32
| 53.48
| 66.08
| 56.95
| 48.83
| 58.67
| 69.75
| 69.8
| Order
|
|
|
|
|
|
|
|
| MetaSim 1
| 36.86
| 57.43
| 87.94
| 62.26
| 42.43
| 62.57
| 91.84
| 91.31
| MetaSim 2
| 44.63
| 66.97
| 90.58
| 72.77
| 52.76
| 71.85
| 94.24
| 92.5
| MetaSim 3
| 32.34
| 50.33
| 93.89
| 61.62
| 39.74
| 58.26
| 94.26
| 61.63
| MetaSim 4
| 24.99
| 56.08
| 99.55
| 61.27
| 30.84
| 65.83
| 100
| 61.27
| iMESS1
| 35.39
| 55.17
| 74.64
| 57.82
| 41.54
| 58.45
| 78.45
| 75.34
| iMESS2
| 37.93
| 56
| 75.72
| 59.08
| 44.47
| 59.38
| 79.58
| 76.7
| Family
|
|
|
|
|
|
|
|
| MetaSim 1
| 33.05
| 52.52
| 86.74
| 56.9
| 36.51
| 54.08
| 90.68
| 87.97
| MetaSim 2
| 36.63
| 57.89
| 87.7
| 62.63
| 42.21
| 62.98
| 91.63
| 91.54
| MetaSim 3
| 24.91
| 40.07
| 93.6
| 49.85
| 29.49
| 46.34
| 94.24
| 49.85
| MetaSim 4
| 15.42
| 47.24
| 99.11
| 47.19
| 18.5
| 55.41
| 100
| 47.19
| iMESS1
| 31.87
| 51.59
| 72.41
| 53.8
| 36.42
| 55.7
| 76.74
| 76.71
| iMESS2
| 34.64
| 50.97
| 72.53
| 53.66
| 39.49
| 54.93
| 76.9
| 77.44
| Genus
|
|
|
|
|
|
|
|
| MetaSim 1
| 33.05
| 52.52
| 86.74
| 56.9
| 36.51
| 54.08
| 90.68
| 87.97
| MetaSim 2
| 32.81
| 53.01
| 86.55
| 57.2
| 36.3
| 54.56
| 90.46
| 88.25
| MetaSim 3
| 24.14
| 40.07
| 93.59
| 49.82
| 27.5
| 45.71
| 94.24
| 49.82
| MetaSim 4
| 14.99
| 47.24
| 99.09
| 47.15
| 17.2
| 54.65
| 100
| 47.15
| iMESS1
| 27.46
| 43.68
| 72.64
| 46.42
| 30.19
| 45.19
| 77.61
| 73.15
| iMESS2
| 28.89
| 42.44
| 73.99
| 45.3
| 31.8
| 44.09
| 79.23
| 74.33
| Species
|
|
|
|
|
|
|
|
| MetaSim 1
| 20.97
| 32.11
| 50.89
| 27.33
| 20.97
| 32.11
| 78.95
| 79.82
| MetaSim 2
| 20.65
| 32.2
| 50.51
| 27.24
| 20.65
| 32.2
| 78.45
| 79.79
| MetaSim 3
| 20.36
| 19.63
| 78.75
| 28.45
| 20.36
| 19.63
| 93.23
| 28.45
| MetaSim 4
| 10.19
| 21.67
| 80.26
| 20.36
| 10.19
| 21.67
| 100
| 20.36
| iMESS1
| 17.92
| 23.41
| 42.49
| 21.19
| 17.92
| 23.41
| 67.73
| 60.72
| iMESS2
| 19.52
| 25.29
| 45.2
| 24.26
| 19.52
| 25.29
| 69.93
| 66.59
| |