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
| |
