TABLE 1.

Performance analysis of sequencing platforms^a

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

^aAll 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.

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

^cManufacturer's data.

^dEstimated calculation for consumables.

^eFor 16 SMRT cells.

^fSee http://www.allseq.com/knowledge-bank/sequencing-platforms/pacific-biosciences/.

^gSee http://lab.loman.net/2017/03/09/ultrareads-for-nanopore/.