Table 1 Comparison among the most used NGS platforms
From: Next-generation sequencing: recent applications to the analysis of colorectal cancer
| Â | Roche | Â | Illumina | Thermo Fisher | Pacific Biosciences | Oxford Nanopore | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
GS Junior | GS FLX + | MiniSeq | MiSeq | NextSeq | HiSeq/HiSeqX | NovaSeq | SOLID 5500W | Ion PGM | Ion Proton | Ion S5 | RS II | Sequel | MinION | GridION/PromethION | |
Max output | 35 Mb | 700 Mb | 7.5 Gb | 15 Gb | 120 Gb | 1500/1800 Gb | 6000 Gb | 320 Gb | 1–2 Gb | 10 Gb | 10–15 Gb | 1 Gb | 10 Gb | 10–20 Gb | 50–100 Gb/ Tb scale |
Max reads/run | 0.1 M | 1 M | 50 M (PE) | 50 M (PE) | 800 M (PE) | 3 G (PE) | 20 G | 1.4 G | 5.5 M | 60–80 M | 3–80 M | 50 Kb | 500 Kb | 2–4 M | 14–1000 M |
Max read length | 400 b | 1000 b | 2 × 150 b | 2 × 300 b | 2 × 150 b | 2 × 150 b | 2 × 150 b | 50 b | 400 b | 200 b | 600 b | 15 Kb (mean read lenght) | 15 Kb (mean read lenght) | 300 K | 300 K |
Accuracy (max) | 99% at 400 b | 99.9% at 15× coverage E. coli | 99.9% for more than 80–85% of bases | 99.9% for more than 75–90% of bases | 99.9% for more than 75–80% of bases | 99% for more than 75–85% of bases | 99.9% for more than 75–85% of bases | > 99% | > 99% | > 99% | 99% (expected) | 99% | 99% | 96% | 96% |
Run time | 10 h | 10–23 h | 7–24 h | 4–56 h | 12–30 h | 1–3.5/<3 days | 19–40 h | 10 days | 2–7 h | 2–4 h | 2.5 h | 0.5–10 h | 0.5–10 h | 2 min–48h | 2 min–48 h |
DNA/RNA inputa | 500 ng | 200 ng | 1–200 ng | 1–100 ng | 50 ng–1 µg | 50 ng–1 µg | 100 ng–1 µg | 10 ng–5 µg | 1–100 ng | 1–100 ng | 1–100 ng | 10 ng–1 µg | 10 ng–1 µg | 200 ng | 200 ng |
Max prep time/ Hands-on | 24 h | 24 h | 1 day/ 4 h | 7 h | 9 h/ 6 h | 2.5 days | 2.5 days | 8 h | 10 h/ 4.5 h | 10 h/ 45 min | 45 min hands-on | 6 h/ 4 h | 6 h/ 4 h | 10 min (1D) | 10 min (1D) |
Key applications | A | B | C | D | E | F/G | F | H | I | L | M | N | O | P | P |