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Table 1 Comparison of STRONG, DESMAN and mixtureS for strain reconstruction in the synthetic community data sets

From: STRONG: metagenomics strain resolution on assembly graphs

Method

Data set

MAGs

#SCGs

#fSCGs

Found

Not F.

Rep.

Err

R2

fG

STRONG

Synth_S03

20

33.18

19.71

45

20

3

0.069

0.81(0.99)

26/38 = 0.68

DESMAN

    

42

23

2

0.125

0.81(1.00)

26/38 = 0.68

mixtureS

    

35

30

8

0.706

—

8/38 = 0.21

STRONG

Synth_S05

21

32.13

22.71

53

13

2

0.062

0.87(0.99)

29/38 = 0.76

DESMAN

    

50

16

9

0.222

0.83(0.96)

20/38 = 0.53

mixtureS

    

38

28

9

0.590

—

7/38 = 0.18

STRONG

Synth_S10

25

32.05

22.72

58

19

0

0.036

0.84(0.99)

30/43 = 0.70

DESMAN

    

58

21

10

0.206

0.79(0.92)

25/44 = 0.57

mixtureS

    

43

36

7

0.279

—

9/44 = 0.20

STRONG

Synth_S15

23

32.17

24.19

60

12

1

0.046

0.87(0.97)

34/42 = 0.81

DESMAN

    

58

14

9

0.144

0.81(0.92)

25/42 = 0.60

mixtureS

    

38

34

16

0.321

—

9/33 = 0.21

  1. Data set: Results are shown for the four different sample numbers. MAGs: The number of MAGs reconstructed with more than two reference strains. #SCGs: The average number of SCGs found in each MAG. #fSCGs The average number of SCGs after filtering in STRONG. Found: Number of strains matched to a reference strain. Not F.: Number of reference strains that had no predicted strain with a closest match to it. Rep.: Number of strains matching to a reference that already has a better match. Err: The average error rate of the ‘Found’ strains in percentage base pairs. R2: Correlation between predicted and actual strain relative proportions given as adjusted R2, the figure in parentheses is when restricted to MAGs where the number of strains was correctly predicted. fG: the fraction of MAGs where the number of strains was correctly inferred