Table 1 Characteristics of several commercially available NGS platforms
From: From next-generation resequencing reads to a high-quality variant data set
Capillary | Next generation | ||||||
|---|---|---|---|---|---|---|---|
Sanger | 454 | Illumina | Ion Torrent | ||||
Platform | 3730xl | GS FLX+ | GS Jr.a | HiSeq X Ten | HiSeq 2500 | MiSeqa | PGM 318a |
Template preparation | Plasmid/PCR | emPCR | emPCR | Solid phase | Solid phase | Solid phase | emPCR |
Run time | ~3 h | ~1 Day | ~10 h | ~3 Days | ~6 Days | ~65 h | ~4–7 h |
Output/run | 0.08 Mb | 700 Mb | 35 Mb | 1.8 Tb | 1 Tb | 15 Gb | 2 Gb |
Read length | 1 kb | 1 kb | 700 b | 2 × 150 b | 2 × 125 b | 2 × 300 b | 400 b |
No. of reads/run | 96 (standard) up to 384 (rare) | 1 M | 0.1 M | 6 B | 4 B | 25 M | 5.5 M |
Error rateb | 0.1–1% | ~1% | ~1% | ~0.1% | ~0.1% | ~0.1% | ~1% |
Primary errors | Substitutions | Indels | Substitutionsc | Indels | |||
Advantages | • Long reads • High quality | • Long reads • Fast run time | • Highest throughput • Low per-base cost | • Unmodified nucleotides • No optical scanning necessary, and thus no photo damage • Fast run time | |||
Limitations | • Low throughput • High costs | • High error rates in homopolymer regions • Low throughput • High costs • Cumbersome emPCR | • Short reads • Random dispersion of clusters can cause poor sequence quality • Underrepresentation of AT-rich and GC-rich regions | • High error rates in homopolymer regions • Cumbersome emPCR | |||
