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Table 2 General characteristics of the three approaches employed in this study

From: Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples

  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) +++ ++ +
  1. aThe price varies greatly with different sequencing output and in different regions