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Having used Kindles, Kobos and a Nook, my opinion is that Kobo devices work best with calibre. There are several automatic things you can have calibre do on your Kobo which aren't possible to do on Kindles and Nooks, for example. Kobos display series info and synopsis for sideloaded books. You can have automatic collections, automatic metadata management, customized subtitle field. You can back up and restore your reading progress (useful when you have to factory reset your device for some reason or change devices).
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