The A, C, G, and T of Genome Assembly

Table 1

Comparison of current (as of Nov. 15, 2014) sequencing platforms. PCR: polymerase chain reaction, SS: sequencing by synthesis, SL: sequencing by ligation, SH: sequencing by hybridization, and SE: sequencing by expansion.

Platform	Biochemistry/; biotechnology	Amplification	Throughput	Reads per run	Read length (bp)	Seq run time	Error rate (%)	Machine cost 1000	Cost per run	Cost per unit data
Sanger (Applied Biosystems 3730xl)	Dideoxynucleotide termination of PCR	PCR	0.06 Mb	9600	1000	2 hrs	0.1	$100	$100	$8,000–$10,000/Gb
454 GS+	Bioluminescence on nucleotide incorporation	Emulsion PCR	70 Mb	70 k100 k	700	18 hours	<1.0	$125	$1,000	$28.50/Gb
454 GS FLX+	Bioluminescence on nucleotide incorporation	Emulsion PCR	700 Mb	1 M	1000	23 hours	<1.0	$500	$6,000	$8.50/Gb
MiSeq	Cleavage of 3′-O-azidomethyl reversible terminator and fluorescent tag on nucleotide incorporation	SS	15 Gb	25 M	2W300	555 hrs	0.1	$125	$1.4K	$93/Gb
HiSeq X Ten	Cleavage of 3′-O-azidomethyl reversible terminator and fluorescent tag on nucleotide incorporation	SS	1000 Gb	4000 M	2W125	7 hrs6 d	0.1	$1,000	$12K	$7/Gb
NextSeq 500	Cleavage of 3′-O-azidomethyl reversible terminator and fluorescent tag on nucleotide incorporation	SS	129 Gb	400 M	2W150	2629 hrs	0.1	$250	$4K	$33/Gb
SOLiD 5500xl	Ligation of octamer oligonucleotide and cleavage of fluorescent tag	SL	180 Gb	2.8 B	2W60	150 hrs	0.01	$595	$10K	$9/Gb
Ion Proton I	Proton sensing by pH change	SS	10 Gb	4080 M	200	24 hrs	1.0	$149	$1K	$100/Gb
Ion PGM 318	Proton sensing by pH change	SS	2 Gb	5 M	400	7.3 hrs	1.0	$52	$750	$350/Gb
Polonator G.007	Cleavage of 3′-ONH2 reversible terminator and fluorescent tag on nucleotide incorporation	SL	10 Gb	—	26	—	N.A	N.A	N.A	N.A
Helicos HeliScope	Single-molecule real-time sequencing	SS	35 Gb	20 M	35	8 hrs	0.5	$1,000	$10K	$330/Gb
PacBio RS II	Single-molecule real-time sequencing	SS	1 Gb	50,000	15,000 bp	3 hrs	15	$700	$400	$1000/Gb