TABLE 4.
Deviation of pathogenic target organism abundance from theoretical known abundance in use case 2. These show two replicates of these samples, each showing deviation from known abundance for 1) host cells alone, 2) extraction 1, a neat viral lysate, 3) spike of a 1:10 dilution of viral lysate in host background, and i4) spike of a 1:100 dilution of viral lysate in host background. Known abundance was set to 100%, as host genome was not included in the custom reference database. Nd= not detected.
| Host only | Infected lysate | Host only | Infected lysate | |||||
|---|---|---|---|---|---|---|---|---|
| Neat | 01:10 | 1:100 | Neat | 01:10 | 1:100 | |||
| Bracken | nd | −82.12% | −83.22% | −92.17% | nd | −84.44% | −94.30% | −99.36% |
| Centrifuge | nd | −4.80% | −36.93% | −85.23% | nd | −.90% | −85.84% | −98.50% |
| CLARK | nd | −1.24% | −11.78% | −58.87% | nd | −.70% | −66.78% | −95.15% |
| DIAMOND | nd | −94.42% | −94.74% | −95.22% | nd | −98.69% | −99.12% | −100.00% |
| HS-BLASTN | nd | −2.57% | −18.05% | −68.57% | nd | .00% | −77.48% | −97.32% |
| Kaiju | nd | −100.00% | −100.00% | −100.00% | nd | −100.00% | −100.00% | −100.00% |
| Kallisto | nd | −77.18% | −79.64% | −90.78% | nd | −82.05% | −90.82% | −100.00% |
| Kraken | nd | −81.57% | −84.82% | −92.93% | nd | −74.88% | −88.64% | −97.44% |
| Kraken2 | nd | −88.58% | −89.85% | −94.82% | nd | −86.11% | −94.44% | −99.37% |
| KrakenUniq | nd | −15.22% | −24.55% | −64.05% | nd | −1.40% | −69.38% | −95.80% |
| Mash | nd | −100.00% | −100.00% | −100.00% | nd | −100.00% | −100.00% | −100.00% |
| MMseqs2 | nd | −2.78% | −53.42% | −92.54% | nd | −37.80% | −88.07% | −99.18% |