(It does offer PDF conversion as well, but I found the results to be not very good, so I read native PDFs on the Kindle.) Additionally, while calibre also does not give you control over the library folder hierarchy and file naming, it at least uses a human-readable hierarchy based on //. I started using calibre, which is primarily intended as an e-reader manager, for that reason, and also for the fact that it allows easy conversion to e-reader file formats from HTML, DOC(X), and also from EPUB (which the Kindle can’t read) to MOBI (which it can). But I don’t like its obtuse, iTunes-like management of your library in a hierarchy of meaninglessly named subfolders, and I also wanted something that could sync my library to my Kindle DX. Enough people love Zotero that I hardly need to sing its praises. I force my first-year seminar students to use it for their research papers, and even upper division students who have not used a reference manager before have their minds blown when they realize they no longer need to keep track of where the commas go in a citation. Zotero is great for reference management and automatic citation. For the last two years, I have used a combination of calibre and Zotero to manage my research sources, mostly PDFs of journal articles.
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