4P06 final

| Platform | Sequencing  Principle | Highest  Capacityper  run;format | Accuracy | Direct  Cost  ($/GB) | Machine  cost | Highlights/error  type |
|----|----|----|----|----|----|----|
| Illumina | SBS, fluorescent | NovaSeqP25B: | >99%,fading | $5 or | Versatile; | High capacity & |
| (2nd Gen) | dNTPs, reversibleterminators, 4Ns at  a time | 150 bp x 2 x 3Bx8= 7.2 Tbp;  SE/PE/ MP;PCR | at the ends | >$50?(72hrs) | >750k | accuracy, PE and MPreads, shortreads;  substitution |
| IonTorrent/  proton(2nd Gen) | SBS, regulardNTPs,  pH changes, 1 N at  atime | S5/S5 L540:200bp x  80M=16Gbp;SR;  PCR | >99%? High  error ratefor  long homo-  polymers | \~$1000  (\~4hrs) | 80K | Cheap reagents,quick  sequencing,lower  capacity/high on  indels |
| PacBio | SBS, fluorescent | Sequel II: 20kb x | 87% insingle | $2000 | 700K | Long reads, higherror |
| (3rd Gen) | dNTPs, all together, | 1.5M =30Gbp,SR; | round read, | (2- 30 | | rate, lower capacity, |
| continuously, noterminators | Single molecule,real time/SMART | 99.9%(HiFi) | hrs) | | DNA methylation | |
| Nanopore | Sequencing by the | PromethION 48: | \~85%? | $2-16 | MinION: | Extremely longreads, |
| (3rd Gen) | current profile of | 1Mb x 50 x200K | | (1 min to | $1K; | excellent mobility, |
| | the passing Ns on | =\~10TB; SR; | | 72 hrs) | PromethIO | DNA methylation, low |
| | the DNA through | single molecule, | | | N 48 | capacity/high error |
| | the pore | real time | | | CapEX:!600K | on substitution &indels |

Comparison of NGS platforms  quality vs read length (bp)

DNA sequencing overview:

Cost per human genome ($3B to $300 in 30 yrs)

Sequencing cheaper than data analysis

Cost

v Cost of sequencing library/sample: very little room for decreasing

v Cost of sequencing ($/GB): decrease with increasing throughput; but  limited by the maximal capacity of indexing

v $300 as the wall?

Ø  Read length

v Read length limit for the platforms: 1MB for ONT

v DNA integrity limit: