Next-generation sequencing instruments are a heterogeneous group of machines with regard to throughput, read-length, accuracy, cost per run, cost per megabase, initial costs, size, and technology.
In terms of size and initial costs, instruments can easily be grouped into smaller instruments, so-called “bench-top sequencers” and high-throughput instruments.
Bench-top sequencers enable any laboratory to perform its own sequencing applications, comparable with real-time PCR. These instruments are also used for more clinically oriented applications in combination with target enrichment, where selected target genes are analyzed in great depth, enabling the detection of rare mutants, or detection of mutants in a heterogeneous sample, such as cancer samples. Currently, the throughput of these instruments is in the range of 10 Mb to 7.5 Gb, but is increasing steadily with the continuous improvements on hardware, software, and reagents.
High-throughput sequencers are well suited for large, genome-wide studies, with capacities of up to 600 Gb per run. Some such platforms with high-throughput and accuracy are associated with relatively short read-lengths, which may be an issue with highly repetitive sequence elements or de novo sequencing of unknown genomes. Conversely, there are instruments with higher read-lengths (up to 2500 bp), but significantly lower accuracy and capacity (90 Mb) and instruments in between (~800 bp, 700 Mb).
Therefore, the application determines the instrument that is best suited.
A new approach is the so-called “nanopore sequencing”. Here, a DNA strand is processed through a synthetic or protein nanopore and changes in the electric current allows identification of the base passing the pore. This will theoretically allow sequencing of a complete chromosome in one step, without the need to generate a new DNA strand.