Generally, taxon detection sensitivity was lower at the species level than at the genus level (Figure 2B). Met

/Generally, taxon detection sensitivity was lower at the species level than at the genus level (Figure 2B). Methods using Greengenes had extremely low species-level sensitivities (Qiime: mean=0.16, SD=0.18; Kraken: mean=0.18, SD=0.13; PathoScope: mean=0.28, SD=0.21), significantly lower than all other methods (see Supplemental Table 3 for pairwise p-values). Among those methods that used Greengenes, PathoScope was significantly more sensitive than either Qiime or Kraken. The most sensitive method at the species level was PathoScope using the Silva reference library (mean=0.86, SD=0.15), followed by PathoScope using RefSeq2018 (mean=0.67, SD=0.16).