Comparing Price and Tech. Specs. of Illumina MiSeq, Ion Torrent PGM, 454 GS Junior, and PacBio RS

Recently multiple groups have compared the performance of current next-gen sequencing technologies.  Independent comparisons of different next-gen sequencing machines have given us a good view of what one can expect from these constantly changing technologies.

Apart from performance,  it is also good to know about price and tech. spec. differences – a much easier aspects of next-gen sequencing technology comparisons. As smaller labs have started thinking about using next-gen sequencing , learning about the costs and tech specs of different sequencing technologies is often the first step. Here is such comparison from two recent publications.

Loman et. al and Quail et. al. have presented a nice comparison of price and technical specifications for the current next-gen sequencing machines by sequencing bacterial genomes.  Both Loman et. al and Quail et. al compared the next-gen sequencing technologies available as of Dec. 2011.  For sure, some aspects of the price/tech. spec comparison will be slightly different.  Here is a brief summary of the pricing and sequencing capability comparisons  done by Loman et. al. and Quail. et. al.

Price and Sequencing Capability Comparison of 454 GS Junior, Ion Torrent PGM, and Illumina MiSeq

Loman et. al. performed a detailed comparison of 454 GS Junior, Ion Torrent PGM, and Illumina MiSeq- the current benchtop next-gen sequencers by sequencing E.Coli. If you are interested in the summary of their findings, visit

Next-Gen SequencerMachine CostCost per runMinimum ThroughputSequencing Run TimeCost Per Mb
Illumina MiSeq$125,000$7501500 Mb (2 x 150 Bases)27 Hours$0.5
454 GS Junior$108,000$1,10035 Mb (400 Bases)8 Hours$31
Ion Torrent PGM - 314 Chip$80,490$22510Mb (100 Bases)3 Hours$22.5
Ion Torrent PGM - 316 Chip$80,490$425100Mb3 Hours$4.25
Ion Torrent PGM - 318 Chip$80,490$6251000Mb3 Hours$0.63

Price and Sequencing Capability Comparison of PacBio RS, Ion Torrent PGM, and Illumina MiSeq

Quail et. al. compared the performance of PacBio RS, Ion Torrent PGM, and Illumina MiSeq  by sequencing multiple bacterial species. Quail et. al. also compared the results from the three sequencing technologies with Illumina GAIIx and HiSeq 2000. For the summary of their findings, visit
Machine CostThroughput Per RunSequencing Cost per GbSequencing Run TimeObserved Error rate
Illumina MiSeq$128,0001.5-2 Gb$50227 Hours0.8%
PacBio RS$695,000100 Mb$20002 Hours12.86%
Ion Torrent -318 Chip$80,0001Gb$10002 Hours1.71%
Illumina GAIIx$256,00030 Gb$14810 Days0.76%
Illumina HiSeq 2000$654,000600 Gb$4111 Days0.26%


  1. Scott Tighe says:

    The error rate of the PacBio is incorrect. As the CCS reads continue, trhe Q score can appoach Q50. Not sure where you got this data but it is misleading


  2. Does the cost per Mb include the yearly machine service fee corrected for the number of potential runs?

  3. Ice Saint says:

    I need to buy an Illumina miseq fgx. Where can I buy it for the cheapest price. Also I think I need to understand the terminologies involved in DNA sequencing e.g. throughput, cost per run, etc. Can someone recommend a site or material to me? Thanks for your support in advance.


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