TABLE 1

Performance analysis of sequencing platformsa

PlatformRead length (bp)Output (Gb)CoveragebRun time (h)No. of readsCost per Gb ($)Consumables cost ($)Instrument cost ($)Error rateDimensions (width × depth × ht) (cm)Source(s) (reference[s])
Sequencing by synthesis
    Illumina MiniSeq Mid Output2 × 150c2.1–2.4c8.617c14 million–16 millionc2,584–2,953d6,201c55,411c0.1% in >80% of base callsc45.6 × 48 × 51.8cIllumina
    Illumina MiniSeq High Output1 × 75c1.7–1.9c6.87c22 million–25 millionc3,264–3,648d6,201c55,411c0.1% in >85% of base callsc45.6 × 48 × 51.8cIllumina
2 × 75c3.3–3.8c13.613c44 million–50 millionc1,632–1,879d6,201c55,411c0.1% in >85% of base callsc45.6 × 48 × 51.8cIllumina
2 × 150c6.6–7.5c26.924c44 million–50 millionc827–940d6,201c55,411c0.1% in >80% of base callsc45.6 × 48 × 51.8cIllumina
    Illumina MiSeq Reagent kit v21 × 36c0.54–0.61c2.24c12 million–15 millionc7,946–8,976d4,847c108,244c0.1% in >90% of base callsc68.6 × 56.5 × 52.3cIllumina
2 × 25c0.75–0.85c3.15.5c24 million–30 millionc5,702–6,463d4,847c108,244c0.1% in >90% of base callsc68.6 × 56.5 × 52.3cIllumina
2 × 150c4.5–5.1c18.324c24 million–30 millionc950–1,077d4,847c108,244c0.1% in >80% of base callsc68.6 × 56.5 × 52.3cIllumina
2 × 250c7.5–8.5c30.539c24 million–30 millionc570–646d4,847c108,244c0.1% in >75% of base callsc68.6 × 56.5 × 52.3cIllumina
    Illumina MiSeq Reagent kit v32 × 75c3.3–3.8c13.621c44 million–50 millionc1,362–1,568d5,174c108,244c0.1% in >85% of base callsc68.6 × 56.5 × 52.3cIllumina
2 × 300c13.2–15c53.856c44 million–50 millionc345–392d5,174c108,244c0.1% in >70% of base callsc68.6 × 56.5 × 52.3cIllumina
    Illumina NextSeq 500 Mid Output2 × 75c16.3–20c71.815c<260 millionc318–391d6,369c266,835c0.1% in >75% of base callsc53.3 × 63.5 × 58.4cIllumina
2 × 150c32.5–39c14026c<260 millionc163–196d6,369c266,835c0.1% in >80% of base callsc53.3 × 63.5 × 58.4cIllumina
    Illumina NextSeq 500 High Output1 × 75c25–30c107.711c<400 millionc312–374d9,347c266,835c0.1% in >80% of base callsc53.3 × 63.5 × 58.4cIllumina
2 × 75c50–60c215.318c<800 millionc156–187d9,347c266,835c0.1% in >80% of base callsc53.3 × 63.5 × 58.4cIllumina
2 × 150c100–120c430.629c<800 millionc78–93d9,347c266,835c0.1% in >75% of base callsc53.3 × 63.5 × 58.4cIllumina
Single-molecule real-time sequencing
    Pacific Biosciences RS II P6-C4 chemistry>20,000c8–16e57.40.5–4c55,000c250–500d4,000e695,00014% errors per base203.0 × 90.0 × 160.0cPacBio, AllSeqf (89)
    Pacific Biosciences Sequel system>20,000c80–160e574.20.5–6c370,000c70–140d11,200e350,00014% errors per base92.7 × 86.4 × 167.6cPacBio, AllSeqf (89)
    Oxford Nanopore MinION Mk1 (1D)>882,00010–20c71.81.67–72c138,00049.95–99.9d999c1,000c12% errors per base10.5 × 3.3 × 2.3cOxford Nanopore Technologies, Loman Labsg (231)
    Oxford Nanopore MinION Mk1 (2D)>882,00010–20c71.81.67–72c138,00049.95–99.9d999c1,000c15% errors per base10.5 × 3.3 × 2.3cOxford Nanopore Technologies, Loman Labsg (231, 232)
    Oxford Nanopore PromethION single flow cell<300,000c233c836.21.67–>72c26 millioncNANA135,000 (PEAP)cNA44.0 × 24.0 × 40.0cOxford Nanopore Technologies
    Oxford Nanopore PromethION 48 flow cells<300,000c11,000c3,9475.81.67–>72c1.25 billioncNANA135,000 (PEAP)cNA44.0 × 24.0 × 40.0cOxford Nanopore Technologies
  • a 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.

  • b Calculated for 96 samples and the genome size of S. aureus strain MRSA252 (2,902,619 bp).

  • c Manufacturer's data.

  • d Estimated calculation for consumables.

  • e For 16 SMRT cells.

  • f See http://www.allseq.com/knowledge-bank/sequencing-platforms/pacific-biosciences/.

  • g See http://lab.loman.net/2017/03/09/ultrareads-for-nanopore/.