Table 1.

Comparison of NGS platforms

Sequencing platformLibrary/template preparationSequencing reaction chemistryMaximum read length, bpRun time, dMaximum throughput per run (total bp sequenced)StrengthsLimitations
Illumina HiSeq 2000Bridging amplificationReverse terminator1002a, 11b95–600 GbdMost widely used platform; large throughputAll samples on flow cell sequenced at same read length
Illumina MiSeqBridging amplificationReverse terminator2500.17a, 1.1b440 Mb–7 GbShort run timesLow number of total reads (∼15 million)
Roche Genome Sequencer FLXEmulsion PCRPyrosequencing4000.40.5–0.6 GbLonger reads; fast run timesHigh reagent cost; lowest number of total reads (∼1 million)
SoLiD/ABI 5500Emulsion PCRLigation sequencing752a, 7b90–300 GbIndependent flow cell lanes; high capacity for multiplexingShort read lengths
Ion Personal Genome MachineEmulsion PCRIon sequencing2000.11 GbShort run times; low-cost scalable machineLow number of total reads (∼11 million)
Complete GenomicsPCR on DNA nanoballsLigation sequencing701220–60 GbComplete service for human sequencingHigh cost per sample; only available for human resequencing
HelicosSingle moleculeReverse terminator55821–35 GbNo amplification biasMachine not widely used; sequencing service available through company
PacBio RSSingle moleculeReal-time1,000<0.1cN/APotential for longest read lengths and shorter run timesHighest error rates

NOTE: Amplification-based and single-molecule sequencing technologies have been referred to as second- and third-generation sequencing technologies, respectively, in the literature (16). The term third-generation sequencing has also been used to refer to near-term nanopore sequencing technologies. Nanopore sequencing is not covered in this review, and readers are directed to an article by Branton and colleagues (90).

Abbreviation: N/A, not applicable.

  • aSingle-end sequencing.

  • bPair-end sequencing.

  • cCompany estimate.

  • dTwo flow cells.