Biology:List of DNA sequencers
The market of DNA sequencer instrument is currently dominated by: Illumina (December 2019), followed by PacBio, MGI/BGI and Oxford Nanopore. There are also offerings from Qiagen GeneReader (as of December 2019) and GenapSys. The majority of sequencers can also produce RNA sequences either directly or via cDNA preparation.
The main considerations for DNA sequencer instruments or sequencing runs are:
- Throughput: total number of bases or reads per sequencing run.
- Cost per base: total cost of producing a certain amount of data (e.g. 1 Gigabase = 10E9 bases) per sequencing run.
- Quality of the basecalls (e.g. Q-score): the probability that a basecall is correct.
- Read lengths / sequence lengths: longer read or sequences are easier to use or interpret.
- Rate of production of data: amount of data produced by a sequencing run per unit of time. This relates to the throughput of the instrument over time to maximise the utilization.
- Cost of the instrument: a high capital cost of a DNA sequencing instrument increases the amortisation time over its lifetime and thus increases the cost per base.
Current platforms
An up-to-date table of current instruments still actively offered is shown:
| Platform | Reads x run: (M) | Read length: (paired-end*, Half of data in reads**) | Run time: (d) | Yield: (Gb) | Rate: (Gb/d) | Reagents: ($) | per-Gb: ($) | hg-30x: ($) | Machine: ($) | Install base | Max theoretical output per day (Gb) | Max total output per day (Gb) from current installbase |
| ILMN iSeq 100 1fcell | 4 | 150* | 0.79 | 1.2 | 0.79 | 650 | 521 | 52100 | 19.9K | 1250 | 1.56 | 1950 |
| ILMN MiniSeq 1fcell | 25 | 150* | 1.00 | 7.5 | 7.5 | 1750 | 225 | 22500 | 65K | 1300 | 7.5 | 9750 |
| ILMN MiSeq 1fcell | 25 | 300* | 2.33 | 15 | 7.5 | 1750 | 108 | 10800 | 99K | 8000 | 7.5 | 60000 |
| ILMN NextSeq 550 1fcell | 400 | 150* | 1.25 | 120 | 100 | 5125 | 41 | 4100 | 250K | 4000 | 100 | 400,000 |
| ILMN HiSeq 2500 RR 2fcells | 600 | 100* | 1.13 | 300 | 106.6 | 13920 | 46 | 4600 | 740K | 0 | 106.6 | 0 |
| ILMN HiSeq 2500 V3 2fcells | 3000 | 100* | 11.00 | 600 | 55 | 35300 | 59 | 5900 | 690K | 0 | 55 | 0 |
| ILMN HiSeq 2500 V4 2fcells | 4000 | 125* | 2.50 | 1000 | 166 | 33800 | 38 | 3800 | 690K | 1000 | 166 | 166,000 |
| ILMN HiSeq 4000 2fcells | 5000 | 150* | 3.50 | 1500 | 400 | 34450 | 25 | 2500 | 900K | 400 | 400 | 160,000 |
| ILMN NextSeq 2000 P3 1fcell | 1200 | 150* | 2.00 | 360 | 150 | 6000 | 16.5 | 1650 | 335K | 255 | 150 | 38,250 |
| ILMN HiSeq X 2fcells | 6000 | 150* | 3.00 | 1800 | 600 | 28440 | 8 | 800 | 1M-1.2M | 400 | 600 | 240,000 |
| ILMN NovaSeq SP 2fcells | 1600 | 250* | 1.58 | 800 | 505.3 | 11700 | 10.5 | 1050 | 985K | 0 | 600 | 0 |
| ILMN NovaSeq S1 2fcells | 3200 | 150* | 1.04 | 1000 | 600 | 14000 | 10.5 | 1050 | 985K | 0 | 600 | 0 |
| ILMN NovaSeq S2 2fcells | 6600 | 150* | 1.50 | 2000 | 1333 | 32400 | 7.7 | 770 | 985K | 0 | 0 | 0 |
| ILMN NovaSeq S4 v1.5 2fcells | 20000 | 150* | 1.83 | 6000 | 3600 | 28800 | 4.80 | 480 | 985K | 1100 | 3600 | 3,960,000 |
| PACB RSII | 0.88 | 20K** | 4.30 | 12 | 2.8 | 2400 | 200 | 24000 | 695K | 44 | 2.8 | 123 |
| PACB 8M Sequel II v2.0 chem 1 flowcell | 4 | 45K-185K** | 1.00 | 30-180 | 25-650 | 1300 | 43.3-7.2 | 3897-648 | 350K | 200 | 650 | 130,000 |
| PACB 64M chip R&D 1 flowcell 2022 | 32 | -- | -- | 750-4500 | -- | 200 | 7-1 | 600-100 | 350K | 0 | 16250 | 0 |
| TMO SOLID 5500 XL | 1400 | 60 | 7.00 | 180 | 30 | 10500 | 58.33 | 7000 | 595K | 0 | 0 | 0 |
| TMO Ion S5 510 1chip | 2 - 3 | 200-400 | 0.21 | 1 | 4.8 | 950 | 950 | 114000 | 65K | 0 | 0 | 0 |
| TMO Ion S5 520 1chip | 3 - 6 | 200-600 | 0.23 | 1 | 4.3 | 1000 | 500 | 60000 | 65K | 0 | 0 | 0 |
| TMO Ion S5 530 1chip | 20 | 200-600 | 0.29 | 4 | 13.8 | 1200 | 150 | 18000 | 65K | 0 | 0 | 0 |
| TMO Ion Genexus GX5 1chip | 48-60 | 200-400 | 1.25 | 9.6-24 | -- | 3500 | 104.2-364.6 | 11196 | 299K | 0 | 0 | 0 |
| TMO Ion S5 540 1chip | 80 | 200 | 0.42 | 15 | 35.7 | 1400 | 93.3 | 11196 | 65k | 0 | 0 | 0 |
| TMO Ion S5 550 1chip | 130 | 200 | 0.50 | 25 | 50 | 1670 | 66.8 | 8016 | 65k | 0 | 0 | 0 |
| ONT Plate Flongle 1fcell=1well (R&D) | -- | 500-2000000 | 3.00 | 0.5/1 | -- | 25/50 | 100-25 | -- | -- | 0 | 0 | 0 |
| ONT SmidgION 1fcell | -- | 500-2000000 | -- | -- | -- | -- | -- | -- | -- | 0 | 0 | 0 |
| ONT Flongle 1fcell 126 channels | -- | 500-2000000 | 0.70 | 1-2 | 1.3 | 90 | 90-45 | 8100-2700 | -- | 0 | 0 | 0 |
| ONT MinION Mk 1B 1fcell 512 channels | -- | 500-2000000 | 3.00 | 17/30-50 | -- | 900-475 | 53-9.5 | 4770-885 | 1K | 4500 | 15 | 67,500 |
| ONT GridION X5 5fcells | -- | 500-2000000 | 3.00 | 85/150-250 | -- | 900-475 | 53-9.5 | 4770-885 | 50K | 100 | 75 | 7,500 |
| ONT P2 PromethION 2fcells | -- | 500-2000000 | 3.00 | 333.33 | 37.5-83 | 1250 | 35-5 | 3500-500 | 110K | |||
| ONT PromethION 24fcells 3000 channels | -- | 500-2000000 | 3.00 | 4000 | 450-1000 | 1600-625 | 20-3 | 1440-382 | 110K | 0 | 2333 | 0 |
| ONT PromethION 48fcells 3000 channels | -- | 500-2000000 | 3.00 | 8000 | 900-2000 | 1600-625 | 20-3 | 1440-382 | 285K | 0 | 4667 | 0 |
| ONT PromethION 48fcells 8300 channels | -- | 500-2000000 | 3.00 | 10000 | 1000-2500 | 1600-625 | 20-2.5 | 1440-382 | 285K | 45 | 5769 | 259,615 |
| MGI DNBSEQ-T10×4RS 8fcells | 230000 | PE150* | 3.50 | 70000 | 20000 | 70000 | 1 | 100 | -- | 1 | 20000 | 20,000 |
| MGI DNBSEQ-T7 4fcells | 20000 | PE150* | 1.00 | 6000 | 6000 | 35000 | 5 | 500 | 1M | 20 | 6000 | |
| MGI DNBSEQ-G400RS 2fcells | 3600 | PE200* | 4.54 | 1440 | 317 | -- | 7 | 700 | 360K | 1 | 130 | -- |
| DNBSEQ-G50 FCL 2fcells | 500 | PE150* | 2.75 | 150 | 60 | -- | -- | -- | -- | -- | -- | -- |
| DNBSEQ-G50 2fcells | 300 | PE100* | 2.00 | 60 | 30 | 21600 | 360 | 43200 | 320K | 1 | 30 | 30 |
| DNBSEQ-E5 1fcell | 5 | 100 | 0.38 | 0.5 | 1 | -- | -- | -- | -- | 1 | 1 | 1 |
| Genapsys 1M Chip | 1 | 150 | 1.17 | 0.2 | 0.2 | 100 | 500 | 60000 | 9.9K | 1 | 30 | 30 |
| Genapsys 16M Chip | 10 - 13 | 300 | 1.17 | 3-3.9 | NA | 299 | 299 | 35880 | 9.9K | 1 | 30 | 30 |
| Genapsys 50M read (2021) | 50 | PE150* | 1.17 | 8 | NA | 599 | 54 | 6480 | 9.9K | 1 | 30 | 30 |
| Genapsys 144M Chip (2021) | 144 | PE150* | 1.17 | 30 | NA | 599 | 27 | 3240 | 9.9K | 1 | 30 | 30 |
| Genapsys 144M Chip (2021) long | 144 | PE250* | 2.00 | 50 | NA | 599 | 12 | 1438 | 9.9K | 1 | 30 | 30 |
| Singular Genomics Systems G4 (2022) | 150 | PE150* | 0.67 | 45 | 67.5 | -- | -- | -- | -- | -- | 67.5 | -- |
Technologies under development
There are several new start-up and larger companies developing methods for DNA sequencing:[1]
| Company | Total Money Raised (MUSD) | Money Raised at IPO or Acquisition (MUSD) | Valuation in last raise or Market Cap (MUSD) | Company Valuation for IPOed companies (MUSD) | Further Info |
| Universal Sequencing Technology | 8 | 0 | 0 | 0 | http://41j.com/blog/2018/07/direct-genomics/ |
| Quantum-SI | 0 | 0 | 0 | 0 | info |
| XGenomes | 0 | 0 | 1 | 0 | http://41j.com/blog/2018/12/quantumsi/ |
| QuantuMDx | 26.3 | 0 | 2 | 0 | https://techcrunch.com/2019/03/15/xgenomes-is-bringing-dna-sequencing-to-the-masses/ |
| iNanoBio | 3.3 | 0 | 20 | 0 | http://41j.com/blog/2018/09/quantumdx/ |
| Centrillion Biosciences | 24.3 | 0 | 54 | 0 | http://41j.com/blog/2018/09/inanobio/ |
| Direct Genomics | 34.8 | 0 | 0 | 0 | http://41j.com/blog/2018/07/centrillion-technologies/ |
| Quantapore | 50.6 | 0 | 93 | 0 | info |
| Ontera | 32.6 | 100 | 0 | -- | |
| LaserGen (acquired) | 85 | 105 | 105 | 0 | -- |
| Stratos Genomics | 55.9 | 0 | 120 | 0 | http://41j.com/blog/2018/11/stratos-genomics/ |
| ReadCoor | 25.5 | 0 | 138 | 0 | -- |
| Roswell Biotechnologies | 38 | 192 | 0 | http://41j.com/blog/2018/09/roswell-biotechnologies/ | |
| Omniome | 60 | 0 | 360 | 0 | info |
References
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