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The IBooks app, which is native to the Ipad can read epub files, so no conversion is needed. The few times I do convert from a different format to epub (using Calibre) I choose Sony Reader for my output settings out of habit because I used to do all my reading on my Sony. Whether or not I convert, I have had no trouble opening any epub files in iBooks. There are other reading apps, but since iBooks serves me well, I haven't explored those other options.
The only thing that might be an issue is DRM containing eBooks. Most books I buy are DRM-free. If they're not, I unlock them. I don't remember if I've read any locked library books on my Ipad.
There are ebook reader apps for the Ipad that have desktop equivalents, such as Stanza and, I believe, GoodReader, but none, as far as I know, for iBooks.
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