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In this work a framework for quantum transport simulation from first principles is introduced, focusing on the coherent case. The model is based on the non-equilibrium Green's function (NEGF) formalism and maximally localized Wannier functions (MLWFs). Any device simulation, here based on two-dimensional (2-D) materials, starts by identifying a representative unit cell, computing its electronic structure with density functional theory (DFT), and converting the plane-wave results into a set of MLWFs. From this localized representation of the original unit cell, the device Hamiltonian can be constructed with the help of properly designed upscaling techniques. Here, a powerful tool called Winterface is presented to automatize the whole process and interface the initial MLWF representation with a quantum transport solver. Its concepts, algorithms, and general functionality are discussed on the basis of a molybdenum disulfide (2-D) monolayer structure, as well as its combination with tungsten disulfide. The developed approach can be considered as completely general, restricted only by the capability of the user to perform the required DFT calculations and to "wannierize" its plane-wave results.