A robust, user-friendly, and automated method to determine quantum conductance in quasi-one-dimensional systems is presented. The scheme relies upon an initial density-functional theory calculation in a specific geometry after which the ground-state eigenfunctions are transformed to a maximally-localised Wannier function (MLWF) basis. In this basis, our novel algorithms manipulate and partition the Hamiltonian for the calculation of coherent electronic transport properties within the Landauer-Buttiker formalism. Furthermore, we describe how short-ranged Hamiltonians in the MLWF basis can be combined to build model Hamiltonians of large (>10,000 atom) disordered systems without loss of accuracy. These automated algorithms have been implemented in the Wannier90 code (Mostofi et al., 2008) [1], which is interfaced to a number of electronic structure codes such as Quantum-ESPRESSO, Ablnit, Wien2k, SIESTA and FLEUR. We apply our methods to an Al atomic chain with a Na defect, an axially heterostructured Si/Ge nanowire and to a spin-polarised defect on a zigzag graphene nanoribbon. (C) 2011 Elsevier B.V. All rights reserved.