Specifically intended to read and annotate scientific papers PDFs, with note functionality, snapshotting, LaTeX (SyncTeX, BibDesk, PDFSync) integration, export, highlight&annotation view and more.

I don't think it will replace the more keyboard-driven sioyek for me but it is a nice alternative.

A self-hostable PDF editor, for page changes resizing, reordering, conversions, image insertion, watermarking and quite a bit more

Another terminal-based slide presentation tool. This one seems nice in that it simply uses markdown and every horizontal rule marks a new slide. Simple, efficient, nice.

Also has a simple guide on how to export slides to pdf on the page.

Small python-gtk application, which helps the user to merge or split PDF documents and rotate, crop and rearrange their pages using an interactive and intuitive graphical interface

A comment on pdf annotation on unix systems. Go to the link for follow-up links to spacemacs and the layer in question:

Zathura is amazing, but if you want to take notes in a more or less zathura style pdf-editor (more than just reader), then I would recommend you to check out Spacemacs with its pdf layer. It has all features that Zathura has, but it adds very strong annotation features, it is mind blowing. You have a pdf-editor right within your vim-like editor. With org-noter you can send annotations directly to your org files (the video uses Emacs bindings, but the Spacemacs project uses a perfect Vim rebuild within Emacs). Spacemacs additionally comes with the amazing org-mode for organizing your notes. Due to the Spacemacs layer system, it is very easily installed (I assume you are on a GNU/linux type of system, as you are already using Zathura). There even exists an option to highlight using the keyboard only, although in this case I find it easier to use the mouse.

Sioyek is a PDF viewer designed for reading research papers and technical books.

Has basic scroll, mark, highlight functionality but an interesting 'portal' one. You link one location in the document to another (opened in another window) and the extra window always displays the closest linked location as you read along. Seems useful for consulting e.g. figures or tables while also reading along the main text at the same time.

Can also be extended for OCR, text-to-speech, auto-download and translation which seems good.

Cross-platform

Docspell is a Document Management System (DMS), a system that asists in organizing your piles of documents, resulting from scanners, e-mails and other sources with miminal effort.

Markdown translator producing HTML5 and roff documents in the ms and man formats. Can also produce latex (pdf) as far as I am aware.

Extract text, metadata and references (pdf, url, doi, arxiv) from PDF. Optionally download all referenced PDFs. - GitHub - metachris/pdfx: Extract text, metadata and references (pdf, url, doi, arxiv) from PDF. Optionally download all referenced PDFs.

search document dumps: ingest and explore in one extensible framework - GitHub - newsdev/stevedore: search document dumps: ingest and explore in one extensible framework

Includes gui and cli options, but as far as I can see not more involved setups like https://github.com/jonaswinkler/paperless-ng .

Differences to ironical paperless:

https://paperless-ng.readthedocs.io/en/latest/index.html#paperless-ng

Another pdf ocr solution, but this one seems to be more of a 'plug-and-play' oriented one.

You simply install the command, invoke it on the cli and it does the ocr'ing and pdf/a'ing for you.
Is also required for the nextcloud ocr workflow.

Interesting reference-manager-like application (i.e. "integrated reading environment").

Interesting features:

• incremental reading (showing & remembering progress per article, allowing bookmarking automation)
• annotation sidebar (automatic creation of color-coded annotation overview, a-la Adobe Reader)
• anki card sync (allows creation of cards directly from annotations and sync to anki, with back reference to annotation context)

Includes gui and cli options, but as far as I can see not more involved setups like https://github.com/jonaswinkler/paperless-ng .

Ways of editing (internal) page numbering of PDFs

Edit and view the structure of PDFs, on the commandline or through JSON and thus gain all sorts of useful information to the makeup of a pdf.

Python library to manipulate PDF page labels.

Meaning: you can change the labelling of page sections (preface getting roman numerals and different numbering scheme than main section, etc)

Should be really useful for later on programatically going to the correct pages and extracting the correct page citations from annotations etc

A command-line tool to turn web pages into beautiful, readable PDF, EPUB, or HTML docs. - danburzo/percollate

Vim+Zathura+Synctex. GitHub Gist: instantly share code, notes, and snippets.