http://www.cd-genomics.com/de-novo-Sequencing.html

de novo sequencing, in which sequencing analysis is performed without the aid of a reference genome, is necessary when sequencing a novel species or novel DNA sequence. Combining the latest next generation sequencing technologies, you can obtain high quality results by sequencing different library types and subsequent state-of-the-art bioinformatics.

de novo Sequencing Features and Benefits:
Reliable genome assembly
Cost effective
High throughput data
Low background
Greater accuracy and broader dynamic range

de novo Sequencing Applications:
Sequencing of unknown genomes or when no reference sequence is available
Samples with expected large structural variation e.g. cancer cells
Microbial sequencing – experimental strains, genomes with high plasticity