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Comparison of Illumina MiSeq, Ion Torrent PGM, 454 GS Junior and PacBio RS

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Illumina MiSeq and IonTorrent PGM Technology and Price Comparison

Multiple studies and groups have compared the performance of current next generation sequencing (NGS) technologies. Independent comparisons of different NGS 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 NGS sequencing technology comparisons. As smaller labs have started thinking about using NGS sequencing, learning about the costs and tech specs of different sequencing technologies is often the first step. Loman et. al and Quail et. al. have presented a nice comparison of price and technical specifications for the current NGS sequencing machines by sequencing bacterial genomes.

Both Loman et. al and Quail et. al compared the NGS sequencing technologies available as of Dec. 2011.  Indeed, some aspects of the price comparison does differ and 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.

 

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.

Next-Gen Sequencer Machine Cost Cost per run Minimum Throughput Sequencing Run Time Cost Per Mb
Illumina MiSeq $125,000 $750 1500 Mb (2 x 150 Bases) 27 Hours $0.5
454 GS Junior $108,000 $1,100 35 Mb (400 Bases) 8 Hours $31
Ion Torrent PGM – 314 Chip $80,490 $225 10Mb (100 Bases) 3 Hours $22.5
Ion Torrent PGM – 316 Chip $80,490 $425 100Mb 3 Hours $4.25
Ion Torrent PGM – 318 Chip $80,490 $625 1000Mb 3 Hours $0.63
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.
Machine Cost Throughput Per Run Sequencing Cost per Gb Sequencing Run Time Observed Error rate
Illumina MiSeq $128,000 1.5-2 Gb $502 27 Hours 0.8%
PacBio RS $695,000 100 Mb $2000 2 Hours 12.86%
Ion Torrent -318 Chip $80,000 1Gb $1000 2 Hours 1.71%
Illumina GAIIx $256,000 30 Gb $148 10 Days 0.76%
Illumina HiSeq 2000 $654,000 600 Gb $41 11 Days 0.26%

Don’t let this data fool you though, as you may at first glance look at PacBio and rule it out for your laboratory. But take into account the read length of PacBio of an outstanding 10-15kb compared to the 100bp of MiSeq and you’ll understand why…..

 

So what does that mean?

A long read length has multiple benefits including: isoform identification and detection, copy number variation, microsatellite identification and ultimately you can see what is shared on a single molecule. I believe over 80% of the current NGS market is Illumina which is saying something….Which platform would you choose?

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  1. PB output per cell these days is 750 Mb to 1 Gb with P6-C4 chemistry. After sample prep costs, the cost per cell varies based on the core lab and locale but you could estimate it by taking a lower cost service provider (e.g. Duke at https://dugsim.net/estimate_cost) and dividing by 2 to account for their labor. Should be closer to $160 / Gb now per cell, depending upon the project.

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