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I have to download S2A images over a large area from 2016 March to 2019 January. Before start downloading data, first I want to know cloud coverage percentages of all the images over this period.

Is there any way to do it either on QGIS or using python code?

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I suggest you try s2cloudless Python package: https://github.com/sentinel-hub/sentinel2-cloud-detector More info here: https://medium.com/sentinel-hub/sentinel-hub-cloud-detector-s2cloudless-a67d263d3025

If you are only interested in rough estimates, there are some faster options: https://www.sentinel-hub.com/faq/best-way-do-cloud-filtering-specific-aoi

(disclaimer: I am working at Sentinel Hub project; the resources above require subscription, but you should be able to to it within the limits of a free trial account)

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