I do not suggest calibre because its like the iTunes of ebooks. Its bloated and very slow for me.
They usually have multiple formats if you bought the books. I would just use the better formats. If you want to read a comic book, just put all the pictures in a zip file and it will be a neat comic book. Ideally you would jailbreak and use a different program to read your books (koreader) but if you can't you are stuck with calibre to convert.
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