Table 1.

Sequencing Platform Comparison

Platform	Amplification	Sequencing	Detection	Read Length	Output per Run	Run Time
Second-generation sequencing platforms
454	Emulsion PCR on beads	Unlabeled nucleotide incorporation	Detection of light emitted by release of PPi	Variable (400 bp for single end sequencing)	400--600 Mbp	10 h
SOLiD	Emulsion PCR on beads	Ligation of 2- base encoded fluorescent oligonucleotides	Fluorescence emission from labeled oligonucleotides	75+35 bp	20--30 Gbp	7 d
Illumina	Array-based enzymatic amplification	Fluorescently labeled end- blocked nucleotide incorporation	Fluorescence emission from nucleotides	2[times]100 bp	100--200 Gbp	8 d
Complete	Rolling-circle replication of short segments of DNA into nanoballs	Ligation of fluorescently labeled oligonucleotide probes	Fluorescence emission from oligonucleotide probes	2[times]35 bp	20--60 Gbp	12 d
Third-generation sequencing platforms
Helicos	NA	Single dye- labeled nucleotides are added sequentially and incorporated by polymerases by use of single DNA molecular templates	Microscopy of fluorescently labeled nucleotides	2[times]25– 55 bp	21--35 Gbp	8 d
Pacific Biosciences	NA	Incorporation of fluorescently labeled nucleotides by polymerases on solid support	Zero-mode waveguide imaging of fluorescent nucleotide incorporation by individual polymerases	2[times]1000 bp	75--100 Mbp (projected); 5--10 Mbp (actual usable sequence)	30 min
Oxford nanopore	NA	Processive endo- or exonuclease activity feeds individual bases or whole DNA strands through protein or solid- state nanopores	Current disruption across nanopore corresponds to nucleotide structure	Variable	Variable	Variable
Ion Torrent	Variable	DNA polymerase incorporation of unlabeled nucleotides added sequentially to solid-state microwells	Solid-state detection of hydrogen ions released by nucleotide incorporation	200 bp	10 Mbp to 1 Gbp	2 h

bp indicates base pair; Gbp, one billion base pairs; Mbp, one million base pairs; PP_i, pyrophosphate; and PCR, polymerase chain reaction.