Table 1

Which sequencing technology to use and when?a

Read length

Read count

Sequence throughputb

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.

Thompson and Milos Genome Biology 2011 12:217   doi:10.1186/gb-2011-12-2-217