Table 1.
Summary of the main differences between the three types of prominent sequencing technologies. We choose the most capable instrument as a representative of each sequencing technology.
| Short Reads | Ultra-long Reads | Accurate Long Reads | |
|---|---|---|---|
| Leading company | Illumina (https://www.illumina.com) | Oxford Nanopore Technologies (https://nanoporetech.com) | Pacific Biosciences (https://www.pacb.com) |
| Representative instrument | Illumina NovaSeq 6000 | ONT PromethION 48 | PacBio Sequel IIe |
| Instrument picture |  |
 |
 |
| Instrument weight | 481 kg | 28 kg | 362 kg |
| Instrument dimension (W × H × D in cm) | 80 × 94.5 × 165.6 | 59 × 19 × 43 | 92.7 × 167.6 × 86.4 |
| Instrument cost1 | 3Y | Y | 1.6Y |
| Read length | 100–300 | 100–2 M | 10 K-30 K |
| Read length in a single data file | Fixed | Variable | Modest Variability |
| Accuracy | 99.9 % | 90 %-98 % | 99.9 %2 |
| Maximum sequencing throughput per run | 6 Tb | 14 Tb | 35 Gb (160 Gb of raw sequencing data)3 |
| Number of flow cells operating simultaneously | 2 | 48 | 1 |
| Hands-on library preparation time | 45 min − 2 h | 10 min-3 h | 6 h |
| Turnaround library preparation time4 | 1.5–6.5 h | 24 h | 24 h |
| Sequencing run time (including basecalling) | 44 h | 72 h | 30 h |
1
Y can be as low as USD 300,000. The cost does not include consumables (e.g., flow cells and reagents) needed for each sequencing run.
2
Consensus accuracy.
3
Per SMRT cell. Sequel IIe can process up to 8 SMRT cells sequentially, slide 25 https://www.pacb.com/wp-content/uploads/HiFi_Sequencing_and_Software_v10.1_Release_Technical_Overview_for_Sequel_II_System_and_Sequel_IIe_System_Users-Customer-Training-01.pdf.
4
Includes both hands-on library preparation time and waiting time.