Table 1.
Comparison among the most used NGS platforms
| Roche | Illumina | Thermo Fisher | Pacific Biosciences | Oxford Nanopore | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GS Junior | GS FLX + |
MiniSeq | MiSeq | NextSeq | HiSeq/HiSeqX | NovaSeq | SOLID 5500W | Ion PGM | Ion Proton | Ion S5 | RS II | Sequel | MinION | GridION/PromethION | |
| Max output | 35 Mb | 700 Mb | 7.5 Gb | 15 Gb | 120 Gb | 1500/1800 Gb | 6000 Gb | 320 Gb | 1–2 Gb | 10 Gb | 10–15 Gb | 1 Gb | 10 Gb | 10–20 Gb | 50–100 Gb/ Tb scale |
| Max reads/run | 0.1 M | 1 M | 50 M (PE) | 50 M (PE) | 800 M (PE) | 3 G (PE) | 20 G | 1.4 G | 5.5 M | 60–80 M | 3–80 M | 50 Kb | 500 Kb | 2–4 M | 14–1000 M |
| Max read length | 400 b | 1000 b | 2 × 150 b | 2 × 300 b | 2 × 150 b | 2 × 150 b | 2 × 150 b | 50 b | 400 b | 200 b | 600 b | 15 Kb (mean read lenght) | 15 Kb (mean read lenght) | 300 K | 300 K |
| Accuracy (max) | 99% at 400 b | 99.9% at 15× coverage E. coli | 99.9% for more than 80–85% of bases | 99.9% for more than 75–90% of bases | 99.9% for more than 75–80% of bases | 99% for more than 75–85% of bases | 99.9% for more than 75–85% of bases | > 99% | > 99% | > 99% | 99% (expected) | 99% | 99% | 96% | 96% |
| Run time | 10 h | 10–23 h | 7–24 h | 4–56 h | 12–30 h | 1–3.5/<3 days | 19–40 h | 10 days | 2–7 h | 2–4 h | 2.5 h | 0.5–10 h | 0.5–10 h | 2 min–48h | 2 min–48 h |
| DNA/RNA inputa | 500 ng | 200 ng | 1–200 ng | 1–100 ng | 50 ng–1 µg | 50 ng–1 µg | 100 ng–1 µg | 10 ng–5 µg | 1–100 ng | 1–100 ng | 1–100 ng | 10 ng–1 µg | 10 ng–1 µg | 200 ng | 200 ng |
| Max prep time/ Hands-on |
24 h | 24 h | 1 day/ 4 h |
7 h | 9 h/ 6 h |
2.5 days | 2.5 days | 8 h | 10 h/ 4.5 h |
10 h/ 45 min |
45 min hands-on | 6 h/ 4 h |
6 h/ 4 h |
10 min (1D) | 10 min (1D) |
| Key applications | A | B | C | D | E | F/G | F | H | I | L | M | N | O | P | P |
A Large–small genome de novo sequencing, resequencing, transcriptome, DNA–protein interaction, methylation, shotgun metagenomics
B De novo complex genome assembly, cDNA/transcriptome assembly, sequence capture, shotgun metagenomics
C Small whole genome, targeted gene seq, targeted gene expression profiling, miRNA and small RNA
D Small whole genome, targeted gene seq, de novo seq, targeted gene expression profiling, miRNA and small RNA, DNA–protein interaction, 16S metagenomic seq
E Large and small whole genome, exome, targeted gene seq, de novo seq, whole transcriptome, gene expression profiling with mRNA-Seq, miRNA and small RNA, DNA–protein interaction, methylation, metagenomic seq
F Large and small whole-genome, exome, targeted gene seq, whole transcriptome, gene expression profiling, small and miRNA, DNA–protein interaction, methylation, shotgun metagenomics
G Human population scale studies, non human whole genome seq
H Whole genome/exome sequencing, de novo seq, targeted resequencing, gene expression, microRNA, ChIP, methylation analysis
I Targeted DNA-RNA seq, microbial sequencing
L Exome-seq, de novo seq, gene expression seq, transcriptome, small RNA seq, ChIP seq
M Targeted gene seq, transcriptome, targeted RNA seq, small RNA, de novo microbial sequencing
N Whole genome sequencing of small genomes, targeted sequencing, complex population analysis, RNA sequencing of targeted transcripts, microbial, epigenetics
O Whole genome de novo assembly, studies for structural variants, transcriptomes, targeted transcript, epigenetic modifications
P De novo sequencing, targeted sequencing, metagenomics, epigenetics
M million, PE paired ends, Mb megabases, Gb gigabases, Tb terabases, b bases
aDepending on the library type