2013 NGS Field Guide – Table 3a – Instrument costs

Table 3a. Instrument purchase cost, additional instrument costs, and service agreement costs for commercially available DNA sequencing platforms in 2012. All costs are list price in thousands of US dollars.

Instrument Purchase Cost Additional Instrumentsa Service Contractb
3730xl (capillary) $376 $19.8
454 GS Jr. Titanium $108 $16 $12.6
454 FLX to FLX+ upgrade $29.5
454 FLX+ $450 $30 $50
PacBio RS $695 $85
Ion Torrent – PGM (314/316/318 chips) $49 $18/32c $7.5/9.9d
Ion Torrent – Proton (chips I, II, III) $224 $19.5/3.3-8.5e $22.4f
SOLiD – 5500xl $251 $54g $44.4h
Illumina MiSeq $125 $12.5
Illumina MiSeq upgrade $0
Illumina HiScanSQ $405 $55i $41.5
Illumina GAIIx $250 $100j $44.5
Illumina HiSeq 1000 $560 $55i $62
Illumina HiSeq 1000 to 2000 upgrade $175
Illumina HiSeq 2000 $690 $55i $75.9
Illumina HiSeq 2000 to 2500 upgrade $50
Illumina HiSeq 2500 $690 $55h $75.9
Oxford Nanopore minION $0k $0 $0
Oxford Nanopore GridION 2000 ?$30?l ? ?
Oxford Nanopore GridION 8000 ?$30?l ? ?

a Does not include general purpose and library preparation equipment (e.g., Covaris [$45k], Agilent bioanalyzer [$18k], thermal cyclers, general purpose centrifuges, MilliQ water, etc.), but includes bead counters for emPCR (up to $20k), TissueLysers or similar for emPCR (up to $10k), specialty centrifuges, etc. when required by the instrument manufacturer. Many labs will need additional general purpose instruments.

b Annual maintenance agreements include on-site service, but do not include extra premiums for the fastest available service

c Required $16.5k Ion Torrent server for conversion of raw signals to base calling; $1k ULTRA-TURRAX®Tube Drive; Argon gas tank (<$0.5k); / cost with $14.5k OneTouch

d Maintenance contract for PGM alone / cost including Server and OneTouch

e Required $75k Ion Torrent server for conversion of raw signals to base calling; Argon gas tank with valves ($0.5k); $14.5k OneTouch

f Maintenance contract for Proton alone / cost including Server and OneTouch

g Includes EZ Bead ePCR automation and required UPS; a Covaris ($45K) is also required but is not included to facilitate comparisons (because one is usually bought with any of the other sequencing systems)

h Includes EZ Bead, Covaris, and one preventative maintenance.

i Cost of cBot (required). Additional instruments for library prep needed (Covaris, etc., similar to 454 FLX)

j Cost of cBot and Paired end module (required for GAIIx)

k minION does not require a separate instrument to operate, it simply plugs into a computer’s USB port & feeds data into the computer.

l Oxford Nanopore has not released a target price for the GridION systems, but this number has been mentioned by multiple sources.

  • Shouldn’t the Ion Proton be 149k$ and not 49k$

    Anyways thanks for updating this truly useful ressource.


  • Travis Glenn

    Thanks for pointing out that typo. It should actually be $224 (because they no longer sell the instrument without the [$75k] analysis computer). It should now be corrected above. Thanks again.

  • Bernie Ball

    Illumina HiSeq 1000 – I cannot find the footnote corresponding to the the superscript “p” in the purchase cost.

    The footnote “g”doesn’t appear to be referenced in the table (I may simply be overlooking it).

  • Travis Glenn

    Footnote “g” should be with the $54k of additional instruments for the SOLID 5500xl.
    Footnote “p” can be ignored (should be deleted), it refers to information that is now on the next line (upgrade cost of HiSeq 1000 to 2000).

  • Ashley

    I’m not sure I’m seeing where the Ion Torrent Proton “Additional instruments” cost is coming from. I looked at the foot notes, but could you break down the $19.5/3.3-8.5 cost for me?

    Also, just to be clear – under additional instruments when there’s a slash, is the upper number is usually the “all-inclusive” number? ie for the PGM is it 49 + 32 for the total cost? Are the additional instruments not required unless specifically noted? Thanks for your time.