Figure - Sequencing Platform Comparison

Choosing a platform by the question being asked.

flowchart TD
  Q{What is the question?} --> A[SNP-level relatedness<br/>outbreak typing]
  Q --> B[Complete genome<br/>plasmid structure]
  Q --> C[Rapid / field / bedside]
  Q --> D[Single gene confirmation]
  Q --> E[Community composition]

  A --> Ill[Illumina short reads<br/>high accuracy, cheap depth]
  B --> Hyb[Hybrid: Illumina + ONT/PacBio<br/>or PacBio HiFi alone]
  C --> ONT[Oxford Nanopore<br/>portable, real-time]
  D --> San[Sanger]
  E --> Meta[Shotgun metagenomics<br/>or 16S amplicon]

  Ill --> Out[[WGS Bioinformatics Pipeline]]
  Hyb --> Out
  ONT --> Out
  Meta --> Out2[[Metagenomics]]

Trade-off summary

Need	Best fit
Lowest cost per base, best per-base accuracy	Illumina
Repeat resolution, circular plasmids	PacBio HiFi or ONT
Turnaround measured in hours, portability	ONT
One amplicon, definitive confirmation	Sanger

Related

• Sequencing Technologies · Genome Assembly · Plasmid and Mobile Element Analysis