The properties and applications of single-molecule DNA sequencing

Table 1 Which sequencing technology to use and when?^a

	Read length	Read count	Sequence throughput^b	Quantitative accuracy	Single pass error rate	Multiple pass error rate	Consensus error rate	Sample manipulations or perturbations	Sample preparation costs	Informatics costs	Optimal single-molecule technology
Genomics
Variant detection			High				High				Helicos
Rare variant detection			High		Moderate	High					Helicos
Whole genome assembly	High		High							High	Mix
Metagenomics	High		High		Moderate					High	PacBio/Starlight
Degraded samples								High			Helicos
Copy number variation		High		High							Helicos
Large structural variations	High										Optical mapping
Transcriptomics
Gene expression		High		High	Moderate			Moderate	High		Helicos
Splicing patterns	High	Moderate		Moderate							PacBio/Starlight
Small RNA quantification		High		High	Moderate			High	High		Helicos
Novel RNA discovery					Moderate		High	High			Helicos

^aThe characteristic features of sequencing technologies are shown, along with a qualitative assessment of how each of those features affect the ease with which an application can be carried out. For example, 'High' indicates that the application requires a high level of the particular feature. This is a general evaluation and particular experiments may vary with respect to the impact of each attribute. The choice of which method to use for a given application depends on the properties of that technology. ^bSequence throughput is defined as read length multiplied by read count.

ISSN: 1474-760X