Table 1.

Advantages and limitations of available Next generation sequencing (NGS) platforms.

Sequencing reaction	Limitation	Advantages	Instruments	Read length in base pairs (bp)	Throughput	Total number of reads	Runtime
Sequencing by ligation or SOLiD sequencing	This sequencing method has been reported to have problems in sequencing particularly palindromic sequences and relatively slower than other methods.	Relatively cheap	SOLiD 5500 Wildfire	50 (SES)	80 Gb	~700 M+	6 days
				75 (SES)	120 Gb
				50 (SES)+	160 Gb
			SOLiD 5500xl	50 (SES)	160 Gb	~1.4 bn+	10 days+
				75 (SES)	240 Gb
				50 (SES)+	320 Gb
			BGISEQ-500 FCS155*	50–100 (SES/PES)+	8–40 Gb+	NA†	24 h
			BGISEQ-500 FCL155	50–100 (SES/PES)+	40–200 Gb*	NA†	24 h+
Sequencing by synthesis:CRT	Equipment are very expensive. Requires high concentration of DNA.	Potential for high sequencing yield, depending upon sequencer model and desired application	Illumina MiniSeq Mid Output	150 (SES)+	2.1–2.4 Gb+	14–16 M+	17 h+
			Illumina MiniSeq High output	75 (SES)	1.6–1.8 Gb	22–25 M(SES)+	7 h
				75 (PES)	3.3–3.7 Gb	44– 50 M(PES)+	13 h
				150 (PES)+	6.6–7.5 Gb+		24 h+
			Illumina MiSeq v2	36 (SES)	540–610 Mb	12–15M (SES)	4 h
				25 (PES)	750–850 Mb	24–30 M (PES)+	5.5 h
				150 (PES)	4.5–5.1 Gb		24 h
				250 (PES)*	7.5–8.5 Gb+		39 h
			Illumina MiSeq v3	75 (PES)	3.3–3.8 Gb	44–50 M (PES)+	21–56 h+
				300 (PES)+	13.2–15 Gb+
			Illumina NextSeq 500/550 Mid output	75 (PES)	16–20 Gb	Up to 260 M (PES)+	15 h
				150 (PES)+	32–40 Gb+		26 h+
			Illumina NextSeq 500/550 High output	75 (SES)	25–30 Gb	400 M(SES)+	11 h
				75 (PES)	50–60 Gb	800 M(PES)+	18 h
				150 (PES)+	100–120 Gb+		29 h+
			Illumina HiSeq2500v2 Rapid run	36 (SES)	9–11 Gb	300 M(SES)+	7 h
				50 (PES)	25–30 Gb	600 M(PES)+	16 h
				100 (PES)	50–60 Gb		27 h
				150 (PES)	75–90 Gb		40 h
				250 (PES)+	125–150 Gb+		60 h+
			Illumina HiSeq2500 v3	36 (SES)	47–52 Gb	1.5 bn (SE)	2 days
				50 (PES)	135–150 Gb	3 bn(PES)+	5.5 days
				100 (PES)+	270–300 Gb		11 days+
			Illumina HiSeq2500 v4	36 (SES)	64–72 Gb	2 bbn(SES)	29 h
				50 (PES)	180–200 Gb	4 B (PES)+	2.5 days
				100 (PES)	360–400 Gb		5 days
				125 (PES)+	450–500 Gb+		6 days
			Illumina HiSeq 3000/4000	50 (SES)	105–125 Gb	2.5 bn (SES)+	1–3.5 days+
				75 (PES)	325–375 Gb
				150 (PES)+	650–750 Gb+
			Illumina HiseqX	150 (PES)+	800–900 Gb per flow cell*	2.6–3 bn (PES)+	< 3 days+
			Qiagen Gene Reader	NA†	12 genes; 1,250 mutations	NA†	Several days
Sequencing by synthesis: SBS	Homopolymer errors	Less expensive and relatively fast	454 GS Junior	Upto 600;400 average (SES,PES)*	35 Mb+	~ 0.1 M+	10 h+
			454 GS Junior+	Upto 1,000;700 average (SES,PES)+	70 Mb+	~ 0.1 M+	18 h+
			454GSFLX TitaniumXLR70	Upto 600;450 mode (SES,PES)+	450 Mb+	~1 M*	10 h+
			454 GS FLX Titanium XL+	Up to 1,000; 700 mode (SE, PE)+	700 Mb+	~1 M+	23 h+
			Ion PGM 314	200 (SES)	30–50	400,000–	23 h
				400 (SES)	60–100 Mb+	550,000+	3.7 h+
			Ion PGM 316	200 (SES)	300–500 Mb	2–3 M+	3 h
				400 (SES)+	600 Mb−1 Gb+		4.9 h+
			Ion PGM 318	200 (SES)	600 Mb−1 Gb	4–5.5 M+	4 h
				400 (SES)+	1–2 Gb+		7.3 h+
			Ion Proton	Up to 200 (SES)	Up to 10 Gb+	60–80 M+	2–4 h+
			Ion S5 520	200 (SES)	600 Mb−1 Gb	3–5 M+	2.5 h
				400 (SES)+	1–2 Gb+		4 h+
			Ion S5 530	200 (SES)	3–4 Gb	15–20 M+	2.5 h
				400 (SES)+	6–8 Gb+		4 h+
			Ion S5 540	200 (SES)+	10–15 Gb+	60–80 M+	2.5 h+
Single-moleculereal-time long reads or (PacificBioSciences)	Moderate throughput and equipment are very expensive	Fast detection	Pacific BioSciences RSII	~20 Kb	500 Mb−1 Gb+	~55,000+	4 h+
			Pacific BioSciences Sequel	8–12 Kb	3.5–7 Gb+	~350,000+	0.5–6 h+
			Oxford Nanopore MK1MinION	Up to 200 Kb	Up to 1.5 Gb	>100,000	Up to 48 h
			Oxford Nanopore PromethION	NA†	Upto 4 Tb+	NA†	NA†

⁺Manufacturer's data;

^*Rounded from Field Guide to next-generation DNA sequencers and 2014 update;

^†Information is not available, as this product has been developed recently.

CRT, Cyclic Reversible Termination; NA, Not Available; PES, Paired End Sequencing; SBS, Sequencing by Synthesis; SES, Single End Sequencing.