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I currently have 2 hard drives, 1 running my Windows OS and all my applications, and another for saving all my chunky media files.

If I was to wipe my hard drive which holds Windows and install Ubuntu on it, would my second NTFS hard drive still work*?

*By work, I mean operate seemlessly as it does in windows; letting me read and write media files with ease.

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Yes, it will work seemlessly. But if you benchmark the performance in both OS, it will be better on windows. Still, most people can't notice that.

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My experience is that NTFS drivers for Linux (including NTFS-3G, which Ubuntu uses) appear less CPU-efficient than the Windows drivers (and probably are). In that sense, they don't perform as well. But that's not the kind of performance most people think of for a filesystem driver. It seems you mean practically speaking, accessing data is actually slower. I recommend clarifying your answer as to what kind of performance you're talking about. (If you have sources to support the claim, you could add them too, but in my opinion even a clarification without sources would improve this answer.) –  Eliah Kagan Apr 12 '13 at 23:32
    
Well, NTFS is not (linux) kernel implemented, is a system implemented in the User Space, there is a penalty in its use. I think it is clear that performance is about read/write speed with average files, he asked about read an write media files, so the answer is related to that. –  migueleon Apr 12 '13 at 23:39

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