Whole genome sequences provide the means to identify genes and determine their role in all types of traits. Yet developing genome-wide physical maps and correlated sequence assemblies is technically challenging and/or costly for many of the more complex genomes. Currently de novo whole genome sequencing strategies are performed using short read technologies and sometimes complemented with long read technologies. Long reads are beneficial for the assembly process but involve higher costs, whereas short reads can be generated at low cost but are more problematic in assembling repeat containing regions. We present a novel strategy that combines genome-wide BAC based physical mapping and whole genome sequence assembly using local assembly and short read technologies. The strategy is build upon the proven Whole Genome Profiling (WGPTM) technology, in which BACs are grouped based on WGP sequence tags, generated from read1. Reverse reads (read2), generated at a random distance from the WGP sequence tags are used to perform local assembly. Following proof of principle in melon and Arabidopsis, we have successfully applied the novel Whole Genome Sequencing strategy to assemble the complex genome of pepper. The results show that the combination of physical mapping and local assembly generates high density sequence scaffolds. It also demonstrates that this approach can be applied to all genomes amenable to BAC library construction. Keygene N.V. owns patents and patent applications covering its Whole Genome, Sequencing and Assembly technologies. WGP is a trademark of Keygene N.V.