Supplementary Table S1: Descriptive and diversity parameters of each simulated dataset. Page 2



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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

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