As there is a requirement ...

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As there is a requirement for filtration and disinfection and the water is going to be used for toilet flushing a low cost approach would be a bag filter as it can be changed easily. 

Rainwater Harvesting, if collected from rooftop is ideally meant for drinking purposes and if you do decide to use the water form drinking purposes then it would be a better idea to go in for a zeolite cartridge that will eradicate the turbidity, followed with an activated carbon filter. 

For disinfection the best choice would be chlorine dioxide as very little is required to get a well disinfected end water quality that would take care of all pathogens as well as eradicate any foul odour.