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Table 1 Comparison among the most used NGS platforms

From: Next-generation sequencing: recent applications to the analysis of colorectal cancer

  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
  1. A Large–small genome de novo sequencing, resequencing, transcriptome, DNA–protein interaction, methylation, shotgun metagenomics
  2. B De novo complex genome assembly, cDNA/transcriptome assembly, sequence capture, shotgun metagenomics
  3. C Small whole genome, targeted gene seq, targeted gene expression profiling, miRNA and small RNA
  4. D Small whole genome, targeted gene seq, de novo seq, targeted gene expression profiling, miRNA and small RNA, DNA–protein interaction, 16S metagenomic seq
  5. 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
  6. F Large and small whole-genome, exome, targeted gene seq, whole transcriptome, gene expression profiling, small and miRNA, DNA–protein interaction, methylation, shotgun metagenomics
  7. G Human population scale studies, non human whole genome seq
  8. H Whole genome/exome sequencing, de novo seq, targeted resequencing, gene expression, microRNA, ChIP, methylation analysis
  9. I Targeted DNA-RNA seq, microbial sequencing
  10. L Exome-seq, de novo seq, gene expression seq, transcriptome, small RNA seq, ChIP seq
  11. M Targeted gene seq, transcriptome, targeted RNA seq, small RNA, de novo microbial sequencing
  12. N Whole genome sequencing of small genomes, targeted sequencing, complex population analysis, RNA sequencing of targeted transcripts, microbial, epigenetics
  13. O Whole genome de novo assembly, studies for structural variants, transcriptomes, targeted transcript, epigenetic modifications
  14. P De novo sequencing, targeted sequencing, metagenomics, epigenetics
  15. M million, PE paired ends, Mb megabases, Gb gigabases, Tb terabases, b bases
  16. aDepending on the library type