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I am considering migrating from SQL Server 2008 to MySQL to save on licencing costs.

I was wanting to know if this would work and what sort of problems it might cause.

As I used EF Code first for the database, my databse is automatically generated based on my class structure. Would this, the entity framework and LINQ still work with a MySQL database?

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Yes EF and LINQ works with MySQL as well, please take a look at these posts.
Entity Framework 5.0 code-first with MySQL Connector 6.6.5.0 on .Net 4.5
and
MySql and Entity Framework Code First

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