  A robust, user-friendly, and automated method to determine quantum
conductance in disordered 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, Comput. Phys. Commun.
178, 685 (2008)], which is interfaced to a number of electronic structure codes
such as Quantum-ESPRESSO, AbInit, 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.
