Erwin L. van Dijk, et al., Ten years of next-generation sequencing technology, Trends in Genetics 30(9), 2014
A drawback of NGS technologies was their relatively short reads. This made genome assembly more difficult and required the development of novel alignment algorithms.
In this latter system, the template DNA is not amplified before sequencing, which places this method at the interface between NGS and the so-called third-generation sequencing technologies. Third-generation methods also allow the detection of single molecules but as an additional common feature sequencing occurs in real time.
For these quantitative applications, Illumina and SOLiD sequencing were more stable than 454, owing to their higher throughput. By contrast, the reads generated by these technologies were initially too short for de novo genome assemblies. Thus, for this type of application, 454 was the preferred technology and enabled exciting discoveries such as the first million bp of a Neanderthal genome.
An exciting new field is single cell genomics. A major objective of this field is to reconstruct cell lineage trees using somatic mutations that arise due to DNA replication errors. Cell lineage trees provide important information and have applications in developmental biology and tumor biology.