© Springer International Publishing Switzerland 2015. This study introduces a method to address the problem of building a draft de novo assembly of complex genomes when a collection of well-assembled long-insert pools is available. Sequencing and assembling a collection of such pools reduces the complexity of the assembly and has been proven to be a viable strategy in order to carry out downstream analyses in recent sequencing projects. In this work we depict a framework to tackle this problem: we propose a novel fingerprinting technique to speed up overlap detection and we describe a merging technique based on the well established string graph structure in order to carry out the reconciliation step. Finally, we show some preliminary results on simulated data sets based on the human chromosome 14 obtained with an early implementation of a tool we called Hierarchical Assemblies Merger.