In this paper we propose a framework to map C-based applications to FPGA-based systems. The framework relies on dependency based analysis information obtained from a high level IR (Intermediate Representation) of the C-Application. The dependencies have a major impact on the instruction flow and the parallelism of the algorithms when implemented on FPGA based high performance computing platforms. We demonstrate the importance of these dependencies in algorithms by examining a compute intensive bio-informatics application. Our place and route results achieved 92% of the clock frequency achieved using a manual design of the same application. The contribution in this paper is to provide a semi-automated approach to generate hardware for FPGA based systems through a high level data dependency graphical IR.