Zotero is a free, open source bibliography manager that supports PDF highlighting. It is the best tool I've found for properly rendering 2-column PDFs common to research publications. Use with the Zotero Integration community plugin by mgmeyers. Requires the [Better BibTeX for Zotero](https://retorque.re/zotero-better-bibtex/installation/) plugin. With Better BibTeX, you can update the unique identifier for each paper. I use the first author's last name and year with an alpha character if multiple papers clipped in the same year. See my [[extras/templates/zotero|zotero]] template.