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I use them both. I prefer the Sony way of grouping books into collections (by creating folders), but that's the only thing I like about it. I think the UI is rubbish, it's unstable, and if it does break, it's a pain to get it back working.
Calibre does everything the Sony software does plus a lot more - format conversion, auto-dpwnload of news sources, editing of metadata, for example. In my experience, it's more reliable too. I can create collection in Calibre too, but it's via editing metadata. much more flexible than the Sony, but less intuitive for me.
One caveat - I do everything on Macs - maybe Windows versions are different
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