A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

Table 1 Technical specifications of Next Generation Sequencing platforms utilised in this study

Platform	Illumina MiSeq	Ion Torrent PGM	PacBio RS	Illumina GAIIx	Illumina HiSeq 2000
Instrument Cost*	$128 K	$80 K**	$695 K	$256 K	$654 K
Sequence yield per run	1.5-2Gb	20-50 Mb on 314 chip, 100-200 Mb on 316 chip, 1Gb on 318 chip	100 Mb	30Gb	600Gb
Sequencing cost per Gb*	$502	$1000 (318 chip)	$2000	$148	$41
Run Time	27 hours***	2 hours	2 hours	10 days	11 days
Reported Accuracy	Mostly > Q30	Mostly Q20	<Q10	Mostly > Q30	Mostly > Q30
Observed Raw Error Rate	0.80 %	1.71 %	12.86 %	0.76 %	0.26 %
Read length	up to 150 bases	~200 bases	Average 1500 bases**** (C1 chemistry)	up to 150 bases	up to 150 bases
Paired reads	Yes	Yes	No	Yes	Yes
Insert size	up to 700 bases	up to 250 bases	up to 10 kb	up to 700 bases	up to 700 bases
Typical DNA requirements	50-1000 ng	100-1000 ng	~1 μg	50-1000 ng	50-1000 ng

* All cost calculations are based on list price quotations obtained from the manufacturer and assume expected sequence yield stated.
** System price including PGM, server, OneTouch and OneTouch ES.
*** Includes two hours of cluster generation.
**** Mean mapped read length includes adapter and reverse strand sequences. Subread lengths, i.e. the individual stretches of sequence originating from the sequenced fragment, are significantly shorter.

ISSN: 1471-2164