Table I.

Brief characterization of some Second Generation Sequencing platforms.

Producer	Roche		Illumina/Solexa			Life Technologies
Platform	454 GS FLX	454 GS Junior	GAII	HISeq models	MiSeq	SOLiD	Ion Torrent	Ion Proton
Seq method	SBS Pyro	SBS Pyro	SBS RDT	SBS RDT	SBS RDT	SBS	SBS H+	SBS H+
Amplification	emPCR	emPCR	Bridge PCR	Bridge PCR	Bridge PCR	emPCR	emPCR	emPCR
Read length	400–700 bp*	400 bp	36–151 bp	up to 2×150 bp**	36–151 bp	35–75 bp	> 100 bp*****	up to 200 bp
Type of read	SE, PE	SE, PE	SE, PE	SE, PE	SE, PE	SE, PE	SE, PE	SE, PE
Output Gb/run	0.45 – 0.7	0.35	≤ 95	up to 600***	> 1	77–155****	> 1*****	up to 10
Run time	up to 24 h	10 h	2–14 days	27h to 11 days	4–27 h	2–7 days	2 h	2–4 h
Error rate (%)	1	1	≥0.1	≥0.1	>0.1	>0.01	~1
Error type	Indels	Indels	Substitutions	Substitutions	Substitutions	Substitutions	Indels
Cost of machine	up to $ 500k	Approx $115k	approx $ 540k	up to $740k	approx $128k	$525k	approx $80k	approx $150k
Pros	Longer reads, faster	Good read length, fast	Widely used, mature platform	Ultra high output, ease of use	Fully automated workflow	Ultra high output, scalable runs; can use 96 bar codes	Cheap, past, label free chemistry, highly scalable	WGS applications, 384 barcodes supported by the Torrent Suite Software
Cons	High cost per Mb, errors with homo polymer repeats	Like the FLX, plus lowest output among small sequencing instruments	High cost per Mb, low multiplexing capabilities	Less scalability, high overall costs	Insufficiently used	Shorter read length, long time for clonal preparation	Homopolymer errors, laborious (yet semi-automated) library preparation	Possibly high cost per Mb and errors

SBS = Sequencing by synthesis; SBL = Sequencing by ligation; RDT = Reverse dye terminator; SE = Single-ended read; PE = Paired-ended read

^*at the lower limit of the range for the Titanium

^**PE for the 1500 and 2500 on rapid run

^***for the 2000 and 2500 on high output

^****155 Gb for the XL model

^*****for the 318 chip