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is it possible to use the MSSQL "BACKUP DATABASE" in a way that will not include the indices, even if they are stored in the same file group as the table itself? Or would I have to move the indices to another filegroup first? Or is there a reason to include indices in the backup?

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There's no backup command without index feature (it's often requested), but Brent Ozar documented his approach here:

http://www.brentozar.com/archive/2010/02/how-to-really-compress-your-sql-server-backups/

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