Table 1.
A comparison between some features of different generations platforms (Solieri et al. 2013)
| Platform | Chemistry | PCR amplification | Starting DNA | Read length | Reads/run | TH/run | Run time | Disadvantages | Applications |
|---|---|---|---|---|---|---|---|---|---|
| Sanger sequencing | Asynchronous with base-specific terminator | Standard PCR | 0.5–1 mg | 700 | Few 1000 bp | 1 Mb | 2 h | PCR biases; low degree of parallelism; high cost of sequencing | Gene/genome sequencing |
| Roche 454 | Sequencing-by synthesis (pyrosequencing) | EmPCR | 1 μg for shotgun library and 5 μg for pair-end | > 400 | 1000,000 | 0.4–0.6Gb | 7–10 h | PCR biases; asynchronous synthesis; homopolymer run; base insertion and deletion errors; EmPCR is cumbersome and technically challenging | De novo genome sequencing, RNA-seq, resequencing/targeted re-sequencing |
| Illumina | Polymerase-based sequencing-by synthesis | Bridge amplification | <1 μg for single or pair-end | 75/2 × 100a | 40,000,000 | 3–6/200 | 3–4 days | PCR biases; low multiplexing capability of samples | De novo genome sequencing, RNA-seq, resequencing/ targeted re-sequencing, metagenomics, ChIP |
| SOLiD | Ligation-based sequencing | EmPCR | <2 μg for shotgun library and 5–20 μg for pair-end | 35–40 | 85,000,000 | 10–20Gb | 7 days | EmPCR is cumbersome and technically challenging PCR biases; long run time | Transcript counting, mutation detection, ChIP, RNA-seq, etc. |
| HeliScope | Polymerase (asynchronous extension | SM; no PCR | <2 μg, single end only | 25–50 | 1000,000,000 | 28Gb | 8 days | Asynchronous synthesis; homopolymer run; high instrument cost; short read lengths; high error rates compared with other reversible terminator chemistries | Resequencing, transcript counting, ChIP, RNA-seq |
| Polonator | Synchronous controlled synthesis | Em PCR | __ | 26 | 160,000,000 | 4.5Gb | 4 days | Low read length; emPCR is cumbersome and technically challenging | Bacterial genome, resequencing, SNPs and structural variants detection |
| PacBio | Phospholinked fluorescent nucleotides | SMRT | ∼1.5 μg (ideally 2–3 μg) | 1000–1200 | 100,000,000 | 100Gb/Hr | 8 h | High instrument cost; low number of sequence read per run; highest error rates compared with other NGS chemistries | De novo genome sequencing, RNA-seq, resequencing/targeted re-sequencing, metagenomics, SNPs and structural variants detection |
| CMOS non-optical sequencing | Template-directed DNA polymerase synthesis | __b | __ | __ | __ | __ | __ | __ | De novo genome sequencing |