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I have a set of points (~2300 bus stops) and I have a network of roads that these bus stops lie on. When I have a bus route that goes from A to B, how do I generate the route such that it follows the underlying road and not just the direct crowfly distance.

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The road data is from OSM and the stop data is user generated. At present the data is hosted on :routemaster.hydlab.in

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You could try my routing script for QGIS Processing based on the core network analysis library. It expects a point layer and a network layer as input and returns a route between the points.:

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