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