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

From: A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome

  Roche 454 Ion Torrent Illumina MiSeq
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