Table 3 GS FLX (Roche), PGM (Ion Torrent, Life Technologies) and MiSeq (Illumina) platform comparison. Data was obtained from the corresponding platform’s website

Sequencing Kit

GS FLX Titanium XLR70

PGM 400 Sequencing

MiSeq Reagent Kits v2

Expected Read Length

Up to 600 bp

Up to 400 bp

MiSeq Reagent Kit v2: Up to 2 × 250 bp

Typical Throughput

450 Mb

Ion 314™ Chip v2: Up to 100 Mb

Ion 316™ Chip v2: Up to 1 Gb

Ion 318™ Chip v2: Up to 2 Gb

Up to 8.5 Gb

Reads per Run

~1000,000 shotgun,

~700,000 amplicon

Ion 314™ Chip v2: 400–550 thousand

Ion 316™ Chip v2: 2–3 millions

Ion 318™ Chip v2: 4–5.5 millions

~15 million reads

Consensus Accuracy

99.995%

99%

99%

Run Time

10 h

Ion 314™ Chip v2: 2.3

to 3.7 h

Ion 316™ Chip v2: 3.0

to 4.9 h

Ion 318™ Chip v2: 4.4

to 7.3 h

4 h and

approximately 39 h

depending on the

number of cycles

Sample Input

gDNA, cDNA, or amplicons (PCR products)

gDNA, cDNA, or amplicons (PCR products)

gDNA, cDNA, or amplicons (PCR products)

Small genome, amplicon, and targeted gene panel sequencing

Weight

532 lbs. (242 kg)

65 lbs. (30 kg)

120 lbs. (54.5 kg)

Instrument cost

~$500 K

~ $80 k

~ $125 k