Table 4 Performance of StrainScan, StrainGE, KrakenUniq, StrainEst, and StrainSeeker for the identification of pathogenic strain of E. coli and M. tuberculosis. Green: consistent results with the ground truth. Red: inconsistent results with the ground truth. “#”: there are multiple hits with identical scores in the output. “R”: the identified strain is the representative strain of the ground truth. Note that StrainSeeker is not able to identify strains of M. tuberculosis and therefore related results are “-”. For StrainSeeker, the number in parentheses represents the number of multiple hits

From: High-resolution strain-level microbiome composition analysis from short reads