Table 3 Analysis of two mock communities from the HMP project. “#”: there are multiple hits with identical scores in the output. “NA”: missing values. Bold font: Mash distance of predicted dominant strain to the truth is \(< 0.05\%\). For StrainSeeker, we took the strain with the smallest Mash distance to the truth as the predicted dominant strain. The two numbers in parentheses represent the number of multiple hits and the average Mash distance between all hits and the ground truth, respectively
From: High-resolution strain-level microbiome composition analysis from short reads
Samples | Tools | Species | Predicted strains | Mash distance to the truth | Running time (s) |
|---|---|---|---|---|---|
SRR172902 (Even) | Krakenuniq | C. acnes | GCF_003384685 | 0.0165552 | 28.89 |
S. epidermidis | GCF_001068615 | 0.0165552 | 34.17 | ||
E. coli | GCF_006364695 | 0.0165552 | 46.09 | ||
StrainSeeker | C. acnes | GCF_000008345 | 0 | 11.42 | |
S. epidermidis | GCF_900458515 (#) | 0.0002398 (3, 0.00027) | 14.21 | ||
E. coli | GCF_000005845 (#) | 0.0000238 (119, 0.00045) | 13.71 | ||
StrainGE | C. acnes | GCF_000008345 | 0 | 146.33 | |
S. epidermidis | GCF_900458515 | 0.0002398 | 192.81 | ||
E. coli | GCF_001308125 | 0.0000476 | 429.02 | ||
StrainEst | C. acnes | GCF_005937545 | 0.0002883 | 743.95 | |
S. epidermidis | GCF_000751035 | 0.0068392 | 57.75 | ||
E. coli | NA | NA | 5307.61 | ||
StrainScan | C. acnes | GCF_000008345 | 0 | 22.61 | |
S. epidermidis | GCF_900458515 | 0.0002398 | 36.94 | ||
E. coli | GCF_002953895 | 0.0000476 | 114.61 | ||
SRR172903 (Staggered) | Krakenuniq | C. acnes | GCF_003384685 | 0.0165552 | 22.79 |
S. epidermidis | GCF_001068615 | 0.0165552 | 17.64 | ||
E. coli | GCF_006364695 | 0.0165552 | 38.76 | ||
StrainSeeker | C. acnes | GCF_000008345 | 0 | 12.45 | |
S. epidermidis | GCF_900458515 (#) | 0.0002398 (3, 0.00027) | 18.31 | ||
E. coli | GCF_000005845 (#) | 0.0000238 (119, 0.00045) | 12.43 | ||
StrainGE | C. acnes | GCF_000008345 | 0 | 175.23 | |
S. epidermidis | GCF_900458515 | 0.0002398 | 232.56 | ||
E. coli | GCF_001308125 | 0.0000476 | 459.44 | ||
StrainEst | C. acnes | NA | NA | 239.08 | |
S. epidermidis | GCF_000751035 | 0.0068392 | 152.02 | ||
E. coli | GCF_000750555 | 0.0000238 | 9414.24 | ||
StrainScan | C. acnes | GCF_000008345 | 0 | 20.49 | |
S. epidermidis | GCF_900458515 | 0.0002398 | 59.26 | ||
E. coli | GCF_002953895 | 0.0000476 | 117.49 |