Table3

Next-generation sequencing platforms

Device	Method	Generation	Major uses	Run time	Length of reads	Reference
Illumina Hi Seq 4000	Flow cell-based, reversible dye termination and four-color optical imaging	2^nd	WES WGS SNP WTA	<1-3.5 days	2×150 bp	^{136,146–151}
Roche 454 pyro-sequencing GS FLX+	Emulsion PCR with bead-based pyro-sequencing and CCD light imaging	2^nd	WGS WTA Targeted Seq SNP	10 h	Up to 1000 bp	^{136,146,151–153}
Life Technologies SOLiD 5500xl	Sequential dinucleotide ligation; flow cell-based four-color optical imaging	2^nd	WES WGS SNP	6 days	2×60 bp	^{136,146,150,151,154}
Life Tech-nologies Ion Torrent PGM	Semi-conductor based nonoptical detection; standard dNTP sequencing chemistry	2^nd	Targeted panel Demand Sequenc-ing	<1 day	400 bp	^136,151,155
Complete Genomics CGA platform	DNA nanoball arrays coupled with combinatori-al probe anchor ligation	2^nd	WGS	Slow: weeks to months	~70 bases	^136,151,156
Pacific Biosciences PacBioRSII	Zero-mode waveguide, individual polymerase; single molecule sequencing using fluorescent dNTPs	3^rd	Long read, full microbial genome	<1-6 h	10-15 kb	^{136,151,157,158}
Seqll Heliscope	True Single Molecule Sequencing, massive parallel sequencing without amplification	3^rd	Targeted WGS WES WTA	~8 h	25-60 bp	^{136,151,156,159}
Nanopore Minion	Nanopore exonuclease sequencing, no need for amplification	3^rd	Long read, full microbial	1 min-48 h	230-300kb	¹⁶⁰
Illumina Hi Seq 4000	Flow cell-based, reversible dye termination and four-color optical imaging	2^nd	WES WGS SNP WTA	<1-3.5 days	2×150 bp	^{136,146–151}
Roche 454 pyro-sequencing GS FLX+	Emulsion PCR with bead-based pyro-sequencing and CCD light imaging	2^nd	WGS WTA Targeted Seq SNP	10 h	Up to 1000 bp	^{136,146,151–153}
Life Technologies SOLiD 5500xl	Sequential dinucleotide ligation; flow cell-based four-color optical imaging	2^nd	WES WGS SNP	6 days	2×60 bp	^{136,146,150,151,154}
Life Tech-nologies Ion Torrent PGM	Semi-conductor based nonoptical detection; standard dNTP sequencing chemistry	2^nd	Targeted panel Demand Sequenc-ing	<1 day	400 bp	^136,151,155
Complete Genomics CGA platform	DNA nanoball arrays coupled with combinatorial probe anchor ligation	2^nd	WGS	Slow: weeks to months	~70 bases	^136,151,156
Pacific Biosciences PacBioRSII	Zero-mode waveguide, individual polymerase; single molecule sequencing using fluorescent dNTPs	3^rd	Long read, full microbial genome	<1-6 h	10-15 kb	^{136,151,157,158}
Seqll Heliscope	True Single Molecule Sequencing, massive parallel sequencing without amplification	3^rd	Targeted WGS WES WTA	~8 h	25-60 bp	^{136,151,156,159}
Nanopore Minion	Nanopore exonuclease sequencing, no need for amplification	3^rd	Long read, full microbial	1 min-48 h	230-300kb	¹⁶⁰

CCD: charge-coupled device; NA: not applicable; NGS: next-generation sequencing; WES: whole exome sequencing; WGS: whole genome sequencing; SNP: single nucleotide polymorphism; WTA: whole transcriptome analysis.