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MongoDB data analytics

This is a general question. I have two collections sitting in two different MongoDB databases. I need to run analytics which is I need compare the two datasets against either for similarities and differences. The documents are heavily nested documents on both sides. There are 5 and 3 mln record in them respectively. I am trying to understand what’s the best way to accomplish this data analysis task? Shall I go with dataframes in python? Or move everything into SQL Server tables and run the analysis there? Or use the native aggregation pipelines of MongoDB from VS Code/python?