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Table 1 Characteristics of second-generation and third-generation sequencing instruments

From: Next-generation sequencing technologies and applications for human genetic history and forensics

Instrument Read length (nucleotides) No. of readsa Output (Gb)a No. of samplesa, b Runtime Advantages Disadvantages
Roche 454 GS FLX+ 700c 1 × 106 0.7 192d 23 h Long reads, short run time Homopolymer errors, expensive
Illumina HiSeq2000 100e 3 × 109 600 384 11 daysf High yield No. of index tags limiting
Life Technologies SOLiD 5500xl 75g 1.5 × 109 180 1,152 14 daysf Inherent error correction Short readsg
Roche 454 GS Junior 400c 1 × 105 0.035 132 9 h Long reads Homopolymer errors, expensive
Illumina MiSeq 150 5 × 106 1.5 96 27 h Short run time, ease of use Expensive per base
Ion Torrent PGM Ion 316 chip > 100h 1 × 106 0.1 16 2 h Short run time, low reagent cost Not well evaluated
Helicos BioSciences HeliScope 35h 1 × 109 35 4,800 8 days SMS, sequences RNA Short reads, high error rate
Pacific Biosciences PacBio RS > 1,000h 1 × 105 0.1 1 90 min SMS, long reads, short run time High error rate, low yield
  1. Most of this information is subject to rapid change, and the aim of this table is not to present absolute numbers but to provide a general comparison between different sequencing systems.
  2. aNumbers calculated for two flow cells on HiSeq2000 and SOLiD 5500xl.
  3. bCalculated as no. of index tags (provided by the sequencing company) × no. of divisions on solid support.
  4. cAverage for single-end sequencing, paired-end reads are shorter.
  5. dNo. of reads decreases when the PicoTiterPlate is divided.
  6. e36 nucleotides for mate-pair reads.
  7. fRun time depends on the read length, and on whether one or two flow cells are used.
  8. gSecond read in paired-end sequencing is limited to 35 nucleotides, and mate pair reads to 60 nucleotides.
  9. hAverage.
  10. SMS = single molecule sequencing.
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