With the increasing number of applications in which a group of organisms associated with a common environment are sequenced, there is an urgent need for a new model for representing the sequenced short reads in a way that takes the nature of these organisms into consideration. In addition to facilitating the assembly process, such new models should allow for easy extraction of other useful biological information from the short reads, including conserved regions among the input genomics, sequence motifs, and other information critical to the recognition and/or classification of the organisms. We present Focus, a new multilayer graph model for short read analysis and extraction of biologically relevant features. The proposed model can be viewed as a data-mining tool that takes advantage of the multilayer graph representation of the reads to extract useful information about the associated genomes/organisms. While not primarily an assembly tool, we assessed Focus using known assemblers with excellent results. We also applied Focus in a case study on a HIV read dataset and were able to successfully extract biologically relevant graph features.