Table 2 General characteristics of the three approaches employed in this study
| Â | Metatranscriptomic sequencing | Hybrid capture-based sequencing | Multiplex PCR amplicon-based sequencing |
|---|---|---|---|
Sequencing objective | Microbiome + human | Target genome | Target genome |
2nd strand synthesis | Y | Y | N |
Fragmentation | Y | Y | N |
Library preparation | Y | Y | N |
PCR | 18 cycles | 18 + 18 cycles | 15 + 25 cycles |
Estimated time for library construction | 10.5 h | 20.5 h | 7.5 h |
Oligo synthesis | – | 120 nt × 506 | 40–60 nt × 2 × (113 + 14 + 10) |
Estimated cost per sample (USD)a | 112.86 | 65.14 | 48.00 |
Estimated minimum data for downstream analyses (base level) | > 10 Gb | Mb | Mb |
Uniformity | High | Moderate | Low |
Sensitivity | + | ++ | +++ |
Accuracy (SNV) | +++ | ++ | +++ |
Accuracy (iSNV) | +++ | ++ | + |