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Backup applications do a good job of backing up large numbers of servers and can generally be made to support application-level backups for common business applications. However, there are a few things Windows PowerShell backup probably does better than most backup applications.
The biggest benefit of Windows PowerShell backup is its high degree of flexibility. For instance, suppose you want to create a one-off backup of every Microsoft Word document on an entire file server. This would be simple to do using PowerShell, but may or may not be possible using a traditional backup application. Even though the majority of backup applications on the market include a mechanism for backing up granular data sets, backup applications usually tend to look at the big picture. It therefore may not be as easy or intuitive to create a copy of a very specific subset of your data.
Another advantage is that a PowerShell backup can sometimes be used to create application-aware backups for applications that are not supported by traditional backup applications. Granted, most of the backup applications on the market support major business applications such as Exchange Server or SQL Server. However, backup applications may not be able to create application-aware backups for custom apps. However, if administrators know the exact requirements for backing up an application, they should be able to build a PowerShell script that will create an application-aware backup.
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