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| Characteristic | MiSeq | PacBio RS II | Ion S5 | HiSeq 4000 | 454 GS FLX Titanium XL+ | SOLiD
5500xl W | Sanger Genetic Analyzer 3500xL |
|
| Instrument price | ~125 K | ~695 K | ~65 K | ~900 K | ~500 K | ~595 K | ~173 K |
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| Sequencing mechanism | Sequencing-by-synthesis | Single-molecule, real-time sequencing | Semiconductor sequencing | Sequencing-by-synthesis | Pyrosequencing | Oligonucleotide
ligation | Dideoxynucleotide chain termination |
|
| Sequencing application | Targeted | Targeted; transcriptome profiling | Targeted; whole exome; transcriptome profiling | Whole exome/genome; transcriptome profiling | Whole exome/genome; transcriptome profiling | Whole exome/genome; transcriptome profiling | Next-generation sequencing validation, targeted sequencing of mutations or small insertions/deletions |
|
| Maximum read length | 300 bp PE | 10,000 bp | 200 bp | 150 bp PE | 700 bp | 75 bp SE, 50 bp mate-paired | 850 bp |
|
| Reads per run | 15 million | 55–900 K | 60–80 million | 2.5–5 billion | ~1 million | 100 million–4.8 billion | Not applicable |
|
| Output data per run | 0.5–15 Gb | 0.5–16 Gb | ~44 Gb | 125–1500 Gb | ~0.7 Gb | 160–320 Gb | 2–100 Kb |
|
| Run time | 4–55 hours | 6 hours | 1-2 days | <1–3.5 days | 23 hours | 2–7 days | 0.5–3 hours |
|
| Advantages | Low error rate; short run time | Long read length; short run time | Short run time; low start-up cost | Low error rate; high throughput | Long read length | Low error rate | Low error rate; long read length |
|
| Disadvantages | Higher cost per base compared to HiSeq instruments | Medium/high cost per base | High error rate for homopolymer tracts and insertions/deletions | Short read length | High error rate for homopolymer tracts | Short read length; long run time | High cost per base; low throughput |
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