TABLE 1.
Comparison of recent long-read and short-read sequencing technologiesa
| Sequencing technology (specifications) | Instrument cost | Library prep cost | Cost per lane/cell | Cost per million reads | Cost per billion bases | Runtime (h) | Throughput (k reads at maximum runtime) | Avg read length (maximum) | Read accuracy (%) | Error profile |
|---|---|---|---|---|---|---|---|---|---|---|
| PacBio Sequel I (maximum 8 cells) | 300,000 | 150–400 | 1,000 | 2,000 | 100 | 10–20 | 500 | 20,000 (50,000) | 85–88/99.9 (CCS) | Homopolymers |
| PacBio Sequel II (maximum 16 cells) | 650,000 | 75–400 | 2,000 | 500 | 17 | 10–30 | 4,000 | 30,000 (100,000) | 88–90/99.9 (CCS) | Homopolymers |
| ONT Flongle | 1,300 | 40–90 | 80 | 400 | 13 | 0.1–12 | 200 | 30,000 (60,000) | 96–99 | Homopolymers |
| ONT MinION | 900 | 90–130 | 600 | 600 | 12 | 0.1–48 | 1,000 | 50,000 (2.3M) | 96–99 | Homopolymers |
| ONT GridION (maximum 5 FCs) | 45,000 | 90–130 | 600 | 600 | 12 | 48 | 1,000 | 50,000 (2.3M) | 96–99 | Homopolymers |
| ONT PromethION (maximum 48 FCs) | 176,000 | 90–600 | 1,400 | 250 | 8 | 72 | 6,000 | 30,000 (330,000) | 96–99 | Homopolymers |
| SLR (example of NovaSeq 2 × 150 PE, 30× coverage, for 5 kb) | 900,000 | 30–50 | 5,000 | 1,250 | 140 | 44 | 4,000 | 9,000 (12,000) | 100 | Unequal coverage |
| Illumina NovaSeq S4 (2 × 150 PE; maximum 4 lanes) | 900,000 | 50–100 | 5,000 | 2.5 | 9 | 44 | 2,000,000 | 250 (290) | 99.9 | Low-quality ends |
| Illumina MiSeq (2 × 300 PE; maximum 2 lanes) | 100,000 | 50–100 | 2,000 | 100 | 175 | 56 | 20,000 | 550 (590) | 99.9 | Low-quality ends |
| ION G5-S5 Prime, P550 chip (maximum 2 chips) | 180,000 | 50 | 700 | 5 | 25 | 6.5 | 130,000 | 200 (250) | 99.0–99.5 | Homopolymers |
| ION G5-S5, P530 chip 600 SE | 60,000 | 50 | 500 | 40 | 70 | 7 | 12,000 | 570 (650) | 99.3–99.7 | Homopolymers, low-quality ends |
| MGI Tech DNBSEQ-T7 (2 × 150 PE; maximum 4 cells) | 990,000 | 50–100 | 6,000 | 1.2 | 4.5 | 24 | 5,000,000 | 250 (290) | 99.9 | Low-quality ends |
| MGI Tech DNBSEQ-G400RS (2 × 200 PE; 400 SE maximum 2 cells × 4 lanes) | 480,000 | 50–100 | 1,800 | 4 | 11 | 108 | 450,000 | 350 (400) | 99.9 | Low-quality ends |
a
Costs are given in EUR. Information is compiled from multiple recent literature sources and price requests from sequencing companies. FC, flow cell; PE, paired-end; SE, single-end.