TABLE 1.
Platform | Read length (bp) | Output (Gb) | Coverageb | Run time (h) | No. of reads | Cost per Gb ($) | Consumables cost ($) | Instrument cost ($) | Error rate | Dimensions (width × depth × ht) (cm) | Source(s) (reference[s]) |
---|---|---|---|---|---|---|---|---|---|---|---|
Sequencing by synthesis | |||||||||||
Illumina MiniSeq Mid Output | 2 × 150c | 2.1–2.4c | 8.6 | 17c | 14 million–16 millionc | 2,584–2,953d | 6,201c | 55,411c | 0.1% in >80% of base callsc | 45.6 × 48 × 51.8c | Illumina |
Illumina MiniSeq High Output | 1 × 75c | 1.7–1.9c | 6.8 | 7c | 22 million–25 millionc | 3,264–3,648d | 6,201c | 55,411c | 0.1% in >85% of base callsc | 45.6 × 48 × 51.8c | Illumina |
2 × 75c | 3.3–3.8c | 13.6 | 13c | 44 million–50 millionc | 1,632–1,879d | 6,201c | 55,411c | 0.1% in >85% of base callsc | 45.6 × 48 × 51.8c | Illumina | |
2 × 150c | 6.6–7.5c | 26.9 | 24c | 44 million–50 millionc | 827–940d | 6,201c | 55,411c | 0.1% in >80% of base callsc | 45.6 × 48 × 51.8c | Illumina | |
Illumina MiSeq Reagent kit v2 | 1 × 36c | 0.54–0.61c | 2.2 | 4c | 12 million–15 millionc | 7,946–8,976d | 4,847c | 108,244c | 0.1% in >90% of base callsc | 68.6 × 56.5 × 52.3c | Illumina |
2 × 25c | 0.75–0.85c | 3.1 | 5.5c | 24 million–30 millionc | 5,702–6,463d | 4,847c | 108,244c | 0.1% in >90% of base callsc | 68.6 × 56.5 × 52.3c | Illumina | |
2 × 150c | 4.5–5.1c | 18.3 | 24c | 24 million–30 millionc | 950–1,077d | 4,847c | 108,244c | 0.1% in >80% of base callsc | 68.6 × 56.5 × 52.3c | Illumina | |
2 × 250c | 7.5–8.5c | 30.5 | 39c | 24 million–30 millionc | 570–646d | 4,847c | 108,244c | 0.1% in >75% of base callsc | 68.6 × 56.5 × 52.3c | Illumina | |
Illumina MiSeq Reagent kit v3 | 2 × 75c | 3.3–3.8c | 13.6 | 21c | 44 million–50 millionc | 1,362–1,568d | 5,174c | 108,244c | 0.1% in >85% of base callsc | 68.6 × 56.5 × 52.3c | Illumina |
2 × 300c | 13.2–15c | 53.8 | 56c | 44 million–50 millionc | 345–392d | 5,174c | 108,244c | 0.1% in >70% of base callsc | 68.6 × 56.5 × 52.3c | Illumina | |
Illumina NextSeq 500 Mid Output | 2 × 75c | 16.3–20c | 71.8 | 15c | <260 millionc | 318–391d | 6,369c | 266,835c | 0.1% in >75% of base callsc | 53.3 × 63.5 × 58.4c | Illumina |
2 × 150c | 32.5–39c | 140 | 26c | <260 millionc | 163–196d | 6,369c | 266,835c | 0.1% in >80% of base callsc | 53.3 × 63.5 × 58.4c | Illumina | |
Illumina NextSeq 500 High Output | 1 × 75c | 25–30c | 107.7 | 11c | <400 millionc | 312–374d | 9,347c | 266,835c | 0.1% in >80% of base callsc | 53.3 × 63.5 × 58.4c | Illumina |
2 × 75c | 50–60c | 215.3 | 18c | <800 millionc | 156–187d | 9,347c | 266,835c | 0.1% in >80% of base callsc | 53.3 × 63.5 × 58.4c | Illumina | |
2 × 150c | 100–120c | 430.6 | 29c | <800 millionc | 78–93d | 9,347c | 266,835c | 0.1% in >75% of base callsc | 53.3 × 63.5 × 58.4c | Illumina | |
Single-molecule real-time sequencing | |||||||||||
Pacific Biosciences RS II P6-C4 chemistry | >20,000c | 8–16e | 57.4 | 0.5–4c | 55,000c | 250–500d | 4,000e | 695,000 | 14% errors per base | 203.0 × 90.0 × 160.0c | PacBio, AllSeqf (89) |
Pacific Biosciences Sequel system | >20,000c | 80–160e | 574.2 | 0.5–6c | 370,000c | 70–140d | 11,200e | 350,000 | 14% errors per base | 92.7 × 86.4 × 167.6c | PacBio, AllSeqf (89) |
Oxford Nanopore MinION Mk1 (1D) | >882,000 | 10–20c | 71.8 | 1.67–72c | 138,000 | 49.95–99.9d | 999c | 1,000c | 12% errors per base | 10.5 × 3.3 × 2.3c | Oxford Nanopore Technologies, Loman Labsg (231) |
Oxford Nanopore MinION Mk1 (2D) | >882,000 | 10–20c | 71.8 | 1.67–72c | 138,000 | 49.95–99.9d | 999c | 1,000c | 15% errors per base | 10.5 × 3.3 × 2.3c | Oxford Nanopore Technologies, Loman Labsg (231, 232) |
Oxford Nanopore PromethION single flow cell | <300,000c | 233c | 836.2 | 1.67–>72c | 26 millionc | NA | NA | 135,000 (PEAP)c | NA | 44.0 × 24.0 × 40.0c | Oxford Nanopore Technologies |
Oxford Nanopore PromethION 48 flow cells | <300,000c | 11,000c | 3,9475.8 | 1.67–>72c | 1.25 billionc | NA | NA | 135,000 (PEAP)c | NA | 44.0 × 24.0 × 40.0c | Oxford Nanopore Technologies |
All quantitative performance measures were taken from previously reported data, as indicated. Consumables costs were calculated as follows: Illumina costs included PhiX Control kit v3, the Nextera XT DNA sample preparation kit (96 samples)/Nextera DNA library preparation kit (96 samples), and Nextera XT Index kit v2 (96 indexes and 384 samples), the highest-output reagent kit. PEAP, PromethION Early-Access Program; NA, no data available.
Calculated for 96 samples and the genome size of S. aureus strain MRSA252 (2,902,619 bp).
Manufacturer's data.
Estimated calculation for consumables.
For 16 SMRT cells.