Which citation manager should you use?

Reading Time: 7 minutes – Updated: January 2022

As researchers, we get through dozens or even hundreds of papers per year. Science has never been bigger - the total global scientific output doubles every nine years - and keeping track of everything can feel impossible at the best of times. This is where citation managers come in!

Keeping an electronic list of papers lets you search, categorise and tag your entire library of papers. Most citation managers let you output reference lists to Word or LaTeX, saving you countless hours of trying to insert references into your own publications. All of the options below integrate with the cloud, so you can access your research library from anywhere - and they all allow you to extend this collaboratively, so that your group/co-authors can share reference lists.

Citation managers are incredibly powerful tools that I think everyone in academia should be using - I’ve found mine essential for keeping track of papers during my PhD. I did a lot of research at the start of my PhD on which citation manager to use which I’ll share below!

But First - Don’t Use Mendeley or EndNote

Mendeley was one of the first citation managers, borne from a London startup in 2008. For a few short years, Mendeley was a major advocate for open access research and collaborative working - all while being provided as a free platform. But in 2013, Mendeley was bought by Elsevier - a company that dominates the research publishing environment by selling research back to institutions at exorbitant costs, giving Elsevier profit margins that are larger than Apple and many big oil companies. In short, Elsevier are the poster child for evil publishing practices in the research community.

It might be tempting to use the most popular citation manager out there, especially if it’s used within your group. But Elsevier do not deserve your support. They’ve been cashing in recently with Mendeley: it is now next to impossible to export your research library away from their platform. So, if you run out of space on their free plan, you’ll be forced to pay up to continue accessing your research library.

For similar reasons, I also can’t recommend EndNote by Clarivate Analytics, who tried to sue a competitor for reverse-engineering their proprietary format that prevented users from moving away from their platform. After much outrage from the scientific community, the lawsuit for $10 million was dropped.

You do not need to give Elsevier or Clarivate Analytics between $50 to $150 a year to access your research library! Keep scrolling to check out four much more ethical (and sometimes even free!) options.

Zotero

• Price: Free (upto 300MB or 15GB with Google Drive)
• OS: Windows / macOS / Linux / 3rd party apps for iOS & Android
• Editor integration: Word, LaTeX, LibreOffice and Google Docs
• Open source

First off is Zotero! It’s one of only two open source and completely free options on this list. It has the widest range of integration options, letting you export references to all major writing tools. And it’s truly cross-platform, even with a Linux app and a fantastic Firefox plugin that lets you save any webpage you come across to Zotero.

The default storage of 300MB isn’t much, but you can use the ZotFile plugin to link your Zotero storage to a cloud server of your choice – such as a free 15GB of data from a Google Drive account.

While there are some flashier features that you don’t get compared to other options on this list – like an integrated PDF annotator or ability to search databases of papers from within the app – it can’t be faulted on the value for money front. I think Zotero is an excellent choice for most researchers, and you’ll be supporting a free and open-source project that benefits the wider research community. If you’re a Linux user (and don’t want to use a browser-based tool) then Zotero is one of only two options for you.

Jabref

• Price: Free (unlimited storage as it’s local)
• OS: Windows / macOS / Linux / 3rd party app for Android
• Editor integration: LaTeX, LibreOffice, Word via a plugin
• Open source

Looking for a simpler free option than Zotero? Jabref has you covered! It’s free and comes with a ton of powerful organisation features, letting you group your library however you please. You can search the literature directly from within the app! Or if you prefer, there are official browser extensions for Firefox, Chrome and Vivaldi.

The big difference with Jabref is that all data is stored locally using BibTeX (the native format for LaTeX references). This has pros and cons: you have essentially limitless storage (because files are kept locally) and it integrates very well with LaTeX – including popular editors like LyX. But it doesn’t have any native cloud synchronisation (unlike everything else on this list!), doesn’t have tools for collaboration, and doesn’t play so nicely with Word (without a bridge between the BibTeX format and Microsoft’s systems.)

If you want a lightweight & free reference manager, write your papers with LaTeX, and only need your library on one computer, then Jabref could be a great choice for you! You could install it right now and quickly get some reference management in your life. Jabref is also the only other tool that has a Linux app.

Paperpile

• Price: $2.99/month (upto 15GB storage with Google Drive) (30 day free trial)
• OS: Windows / macOS / iOS / Android / all browsers
• Editor integration: Word, LaTeX and Google Docs
• Not open source

Are you an avid Google products user? Next on the list is Paperpile, which integrates seamlessly with your Google Drive to give you up to 15GB of free storage from the get go. The modest monthly subscription gives you access to a range of powerful features, such as searching for new references from within the app – all with a (clean and organised UI)[https://paperpile.com/features/reference-manager] that can even let you colour-code your research library.

Some of the other options on this list are major software offerings by big companies. If that isn’t your thing, then I get the impression that Paperpile is a newer, cleaner option that could sit beautifully in your workflow (for less than half the cost of a Netflix subscription). For Google Docs users, it seems like Paperpile is the most bothered about Google Docs integration, which could make it an excellent choice for you.

ReadCube Papers

• Price $5/month or $3/month for students (30 day free trial)
• OS: Windows / macOS / iOS / Android / all browsers
• Editor integration: Word, LaTeX and Google Docs integration
• Not open source

Still not happy? Do you still want more power? ReadCube’s Papers gives you even more search tools and integration with your web browser.

In particular, personalised recommendations and lists of related articles could come in extremely handy in finding new papers for you to read and/or cite with minimal effort. This could come in especially handy if your field has a high turnover rate of new papers in many different journals. Once Papers knows what you’re interested in, it could prevent you from ever missing any important research.

Finally, the Word and Google Docs plugin – SmartCite – looks powerful and fast. If you want your citation manager to help you find new papers and especially if you want to work efficiently within Word, then maybe Papers is the right choice for you.

Citavi

• Price: See if your uni has a site license / €120 for students
• OS: Windows only!
• Editor integration: Word, LaTeX
• Not open source

Citavi is an older but still much-loved option for citation management. It has a free version, although it’s limited to only storing 100 papers (which really makes the free version more of a trial.) It has nice organisation options, but doesn’t have some of the powerful search functionality that other options on this list have. It also only has a Windows desktop app (although you could make it run on a Mac.)

The biggest advantage of Citavi, in my opinion, is if your university already has a site-wide license. It could be a great tool for you to use if you can already use it without needing to commit to spending anything, and if you want a reliable solution you could get running within an hour from finishing reading this blog post. Your university might even already run training sessions on how best to use it!

Final Remarks

That’s a wrap! I hope that this was helpful. There are a few other citation managers that I left off of this list, often because I don’t think they’re still being actively developed.

Do you use a citation manager? Is there anything I missed when writing this article up? Get in touch over on Twitter!

You might also be interested in a blog post I wrote with tablet recommendations for reading and annotating papers.