Table 5 The identification results of 7 tools on one metagenomic dataset containing the low-depth virulent Clostridioides difficile strains. “NA”: missing values. “TcdA” and “TcdB”: two important genes of the virulent C. difficile strains. The presence of “TcdA” and “TcdB” is verified using the Carbohydrate-Active enzymes database [64]
From: High-resolution strain-level microbiome composition analysis from short reads
Tools | Identified dominant strain | # of identified strains | TcdA | TcdB |
|---|---|---|---|---|
StrainScan | GCF_015238635 | 1 | \(\checkmark\) | \(\checkmark\) |
StrainGE | GCF_002234355 | 1 | X | X |
Krakenuniq | GCF_016767015 | 11 | \(\checkmark\) | \(\checkmark\) |
Pathoscope2 | GCF_018885065 | 26 | \(\checkmark\) | \(\checkmark\) |
Sigma | GCF_002812605 | 15 | \(\checkmark\) | X |
StrainEst | NA | NA | NA | NA |
StrainSeeker | NA | NA | NA | NA |