2013 NGS Field Guide – Table 2b – Costs/run, cost/MB, minimum costs

Table 2b. Comparison of costs for all common commercially available 2nd and 3rd generation sequencing platforms, sorted by cost/MB.

Instrument Reagent Cost/runa Reagent Cost/MB Minimum Unit Cost (% run)b
3730xl (capillary) $144 $2,308 $6 (1%)
454 GS Jr. Titanium $1,100 $22 $1,500 (100%)
PacBio RS ≥ $300c $2-17 $500 (100%)
454 FLX Titanium $6,200 $12 $2,000 (12%)
454 FLX+d $6,200 $7 $2,000 (12%)
Ion Torrent – ‘314’ chip $539 $5 ~$750 (100%)
Ion Torrent – ‘316’ chip $739 $1.20 ~$1,000 (100%)
Oxford Nanopore minion * ≤ $900 $1 ~$1,100 (10%)
Illumina MiSeq $1,040 $0.70 ~$1,400 (100%)
Ion Torrent – ‘318’ chip $939 $0.60 ~$1,200 (100%)
Illumina GAIIx $17,575 $0.19 $2,500 (14%)
Illumina MiSeq – version 2 $1,070 $0.14 $1,400 (100%)
Illumina iScanSQ $12,750 $0.09 $2,500 (14%)
Ion Torrent – Proton I $1,050 $0.09d ? (100%)
SOLiD – 5500xl $10,503e < $0.07 $2,000 (12%)
Illumina HiSeq 2500 – rapid * $6,145f $0.05 ? (50%)
Illumina HiSeq 1000 $10,220 $0.04 $2,600 (12%)
Illumina HiSeq 2000 $23,470e ≥$0.04 $2,400 (6%)
Oxford Nanopore GridION 2000 * varies [$0.04] ? (≤1%)
Ion Torrent – Proton II * [$1,000] [$0.02] ? (≤100%)
Oxford Nanopore GridION 8000 * varies $0.02 ? (≤1%)
Ion Torrent – Proton III * [$1,000] [$0.01] ? (100%)

aIncludes all stages of sample prep. for a single sample (i.e., library prep through sequencing; capillary = sequencing only)

bTypical full cost (i.e., including labor, service contract, etc.) of the smallest generally available unit of purchase at an academic core lab provider for the longest available read (and percentage of reads relative to a full run, rounded to the nearest whole percentage)

cLibrary preps cost from $200-$1600 per sample, which can be used for 20 to 2 runs (circular consensus to strobed reads, respectively), thus the cost/MB from multiple runs/library is substantially less.

dIon Torrent only specifies a yield of 10 Gb ($0.10/Mb), but an average output of 70 million reads of 400 bases would result in a yield of 14 Gb ($0.08/Mb).

eMore reads are obtained than is needed from any single sample within most experiments, but the value illustrates the costs.

fReagent costs for 2 x 100 base reads; prices for 2 x 150 base reads are not yet available

? = Detail not yet available

  • = Platform not yet released, values from company press releases is given; extrapolated author speculation [in brackets]