Table 2.

Comparison of sequencing instruments

Characteristic	MiSeq	PacBio RS II	Ion S5	HiSeq 4000	454 GS FLX Titanium XL+	SOLiD 5500xl W	Sanger Genetic Analyzer 3500xL
Instrument price	~$125 K	~$695 K	~$65 K	~$900 K	~$500 K	~$595 K	~$173 K
Sequencing mechanism	Sequencing-by-synthesis	Single molecule, real-time sequencing	Semiconductor sequencing	Sequencing-by-synthesis	Pyrosequencing	Oligonucleotide ligation	Dideoxynucleotide chain termination
Sequencing application	Targeted	Targeted; transcriptome profiling	Targeted; whole exome; transcriptome profiling	Whole exome/genome; transcriptome profiling	Whole exome/genome; transcriptome profiling	Whole exome/genome; transcriptome profiling	Next-generation sequencing validation, targeted sequencing of mutations or small insertions/deletions
Maximum read length	300 bp PE	10,000 bp	200 bp	150 bp PE	700 bp	75 bp SE, 50 bp mate-paired	850 bp
Reads per run	15 million	55 – 900 K	60 – 80 million	2.5 – 5 billion	~1 million	100 million–4.8 billion	Not applicable
Output data per run	0.5 – 15 Gb	0.5 – 16 Gb	~44 Gb	125 – 1500 Gb	~0.7 Gb	160 – 320 Gb	2 – 100 Kb
Run time	4 – 55 hours	6 hours	1 – 2 days	<1 – 3.5 days	23 hours	2 – 7 days	0.5 – 3 hours
Advantages	Low error rate; short run time	Long read length; short run time	Short run time; low start-up cost	Low error rate; high throughput	Long read length	Low error rate	Low error rate; long read length
Disadvantages	Higher cost per base compared to HiSeq instruments	Medium/high cost per base	High error rate for homopolymer tracts and insertions/deletions	Short read length	High error rate for homopolymer tracts	Short read length; long run time	High cost per base; low throughput

bp, base pairs; Gb, gigabases; K, thousand; Kb, kilobases; PE, paired-end; SE, single-end.