The initial generation of the primary genetic sequence of a particular organism is called de novo sequencing. A detailed genetic analysis of any organism is possible only after de novo sequencing has been performed. 

With its long read lengths and high accuracy, capillary electrophoresis-based sequencing is the gold standard technology for de novo projects.  However, the throughput of these systems makes de novo assembly of most organisms a lengthy and costly endeavor. Next-generation sequencing technologies hold great promise in reducing the time and cost of sequencing. 

De novo assembly of small organisms using the SOLiD™ 3 Plus System
The longer read lengths and new data analysis software of the SOLiD™ 3 Plus System enable the de novo assembly of small organisms.  Researchers have demonstrated the assembly of 50bp reads into a scaffold that can then be filled in with capillary electrophoresis-based sequencing.   

SOLiD™ System facilitates the assembly of difficult genomic regions.
For larger organisms, capillary electrophoresis-based sequencing is the preferred platform for scaffold generation.  Once a scaffold is created the SOLiD™ System can be used to fill in the gaps at high coverage.