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If you don't mind an Electron or web-based app with a subscription, you could also look at Zenreader [0], Polar [1] or maybe even Readwise [2]. Zotero will also have a PDF Reader app with Markdown export soon [3]. And some cross-platform note taking / PKM apps also have some kind of PDF annotation support (directly: Logseq [4]; via plugins: Obsidian [5], Roam Research [6]). That said, all these apps are very... - Source: Hacker News / about 2 years ago
I bumped into https://zenreader.co.uk ages ago but never tried it. Source: almost 3 years ago
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Qiqqa - Qiqqa is a free research and reference management software. It can be used in many organizational projects from the academic to the personal to the business endeavor. Read more about Qiqqa.
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .
ZoteroBib - ZoteroBib is a free service to help people quickly create bibliographies without installing any...
Citavi - Citavi is a program for Microsoft Windows that manages literary references and organizes organizational knowledge.
BibDesk - BibDesk is an organizational software created to help you edit and manage your bibliography. It keeps track of your bibliographic information as well as said information's associated web links and files. Read more about BibDesk.