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The only iPad app that Calibre can interface directly with via USB is iBooks as this is the only one that iTunes directly supports.
having said that there is the (free) eBook-Search app on iOS that can interface via WiFi or 3G with the Calibre Content server to select and download books, and having downloaded a book transfer the book to an apporpriate app for the format downloaded (if multiple apps support the format you are asked to choose one). You can also do this using the Safari browser although is not as convenient.
If you are using the Kindle app you also have options such as emailing a book to your Kindle account which would result in the Kindle app downloading it.
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