Journal of Dental Hygiene Science : eISSN 2233-7679

Table 1

Comparison of Next-Generation Sequencing Platforms

 Machine (manufacturer)  Chemistry  Modal read lengtha (bases)  Run time  Gb per run  Current, approximate cost (US$)b  Advantages  Disadvantages
High-end instruments454GS FLX+(Roche) Pyrosequencing 700~800 23 h 0.7 500,000 • Long read lengths • Appreciable hands-on time • High reagent costs • High error rate in homopolymers
HiSeq 2000/2500(Illumina) Reversible terminator 2×100 11 d (regular mode) or 2 (rapid run mode)c 600 (regular mode) or 120 (rapid run modec 750,000 • Cost-effectiveness • Steadily improving read lengths • Massive throughput • Minimal hands-on time • Long run time • Short read lengths • HiSeq 2500 instrument upgrade not available at time of writing (available end 2012)
5500xl SOLiD (Life Technologies) Ligation 75+35 8 d 150 350,000 • Low error rate • Massive throughput • Very short read lengths • Long run times
PacBio RS (Pacific Biosciences) Real-time sequencing 3,000 (maximum 15,000) 20 min 3 per d 750,000 • Simple sample preparation • Low reagent costs • Very long read lengths • High error rate • Expensive system • Difficult installation
Bench-top instruments 454GS Junior (Roche) Pyrosequencing 500 8 h 0.035 100,000 • Long read lengths • Appreciable hands-on time • High reagent costs • High error rate in homopolymers
Ion Personal Genome Machine (Life Technologies) Proton detection 100 or 200 3 h 0.01~0.1 (314 chip), 0.1~0.5 (316 chip) or up to 1 (318 chip) 80,000 (including OneTouch and server) • Short run times • Appropriate throughput for microbial applications • Appreciable hands-on time • High error rate in homopolymers
Ion Proton (Life Technologies) Proton detection Up to 200 2 h Up to 10 (Proton I chip) or up to 100 (Proton II chip) 145,000+75,000 for compulsory server • Short run times • Flexible chip reagents • Instrument not available at time of writing
MiSeq (Illumina) Reversible terminator 2×150 27 h 1.5 125,000 • Cost-effectiveness • Short run times • Appropriate throughput for microbial applications • Minimal hands-on time • Read lengths too short for efficient assembly

Adapted from the article of Loman et al. (Nat Rev Microbiol 10: 599-606, 2012)17) with original copyright holder’s permission.

Average read length for a fragment-based run.

Approximate cost per machine plus additional instrumentation and service contract16).

Available only on the HiSeq 2500.

J Dent Hyg Sci 2019;19:86-95 https://doi.org/10.17135/jdhs.2019.19.2.86
© 2019 J Dent Hyg Sci