Table 2.
Summary of the available NGS platforms in pathogens detection currently.
| Platform | Maximum Read Length [bp] | Maximum Reads per Run | Maximum Output | Run Time (hours) |
Advantages | Disadvantages | Reference |
|---|---|---|---|---|---|---|---|
| Illumina NextSeq 550 | PE150 | 400 million | 120 Gb | 12–30 | Moderate throughput and short running time | Short read length | [14], [67] |
| Illumina NextSeq 1000 & 2000 | PE150 | 1.1 billion | 330 Gb | 11–48 | High throughput | Short read length | [73] |
| Illumina NovaSeq | PE250 | 20 billion | 6 Tb | 13–44 | High throughput and long read length | Long running time | [74], [75] |
| MGISEQ-200 | PE150 | 100 million/ 500 million |
150 Gb | 9–40 | Low cost and high accuracy | Short read length | [76] |
| MGISEQ-2000 | SE400/PE200 | 1500–1800 million | 1440 Gb | FSC: 17–37; FCL:17–109 |
Low cost, high throughput and accuracy | Short read length and long running time | [77] |
| Ion GeneStudio S5 | 600 | 130 million | 15 Gb | 3–21.5 | High compatibility and short running time | Long read length | [78] |
| Oxford Nanopore MinIon |
> 4 Mb | / | 50 Gb | Up to 72 |
Long read length, portable and real time analysis | Low accuracy and high cost | [79] |
| PacBio Sequel system | 1–1.8 Kb | / | 3.5–7 Gb | Up to 20 |
Long read length and short running time | Low accuracy and high cost | [80] |