I am using MODIS NDVI product (MOD13Q1) for the vegetation changes study. I want to remove cloudy or bad pixel from MODIS NDVI data. I am not getting any suitable method or software or any program to do this task.
Although it requires signing up for an account, you can do this through Google Earth Engine's API quite easily. They give comprehensive tutorials and scripts for how to do so, as well as the data products you are asking for. You can remove the cloudy/bad pixels from the NDVI product by adjusting the script of this tutorial for the data layers you'd like to use: https://developers.google.com/earth-engine/ic_composite_mosaic