TABLE 3.
Deviation of pathogenic target organism abundance from theoretical known value in use case 1. Values are representative of samples containing all 10 possible components at equal genome copy input. Nd= not detected.
| Number of expected taxids identified in output (max = 9) | Calculated B. anthracis abundance (theoretical max = 10%) | |||
|---|---|---|---|---|
| Illumina | ONT | Illumina | ONT | |
| Bracken | 1 | 1 | nd | nd |
| Centrifuge | 5 | 4 | nd | nd |
| CLARK | 1 | 1 | nd | nd |
| DIAMOND | 1 | 1 | nd | nd |
| HS-BLASTN | 9 | 9 | 19.20 | 10.65 |
| Kaiju | 1 | 0 | nd | nd |
| Kallisto | 9 | 7 | 0.09 | nd |
| Kraken | 9 | 9 | 0.22 | 0.34 |
| Kraken2 | 9 | 9 | 0.10 | 0.11 |
| KrakenUniq | 9 | 8 | nd | nd |
| Mash | 0 | 0 | nd | nd |
| MMseqs2 | 9 | 8 | nd | nd |