6 Tips on How to Choose Reference Management Software

It appears that I’ve been living a very sheltered life as far as reference management software goes. My institution has a licence for Endnote so I’ve always just used that if I used software at all! As I’ve started researching, I’ve found loads of different reference management systems, and it seems like it’s impossible to pick between them.

I’ve made a list of the reference managers that look useful and I would like to try out. Find them at the bottom of the post.

I have some experience with Endnote and to be honest, that’s what I’m using right now because it’s what is used at my institution and I know many other people that use it and can help with any problems.

However, I have had a bit of a play around with Mendeley and I have been very impressed and in many regards, it seems better than Endnote. I will post up some demonstrations soon.
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So what do I do, change or stick to what I know?

Now all this choice to me seems quite overwhelming and if you’re about to start a project or you’re in the middle of writing one then you probably need to start straight away without spending hours and hours trialling every single one.

Here are some tips to help you choose quickly and effectively:

1. Ask the people in your group what they use. If everyone in your department uses one reference manager, you’ll need a pretty good reason to choose something else so if time is short, it’s probably better to just go with the flow.

2. Have a look at the screenshots on the website of the individual reference manager. Don’t like what you see? Bin it and use something else. If there are no screen shots or no video tour, this is also a bad sign and may show things are getting a little out of date!

3. Type the name of the reference manager into YouTube. If there are loads of how-to videos this is a good sign, if there aren’t, forget about it.

4. Use Google – type the name of your reference software followed by review or forum and see what kind of results you get back.

5. Is it compatible with your operating system? This could be a huge help as not all the reference managers are compatible with all the operating systems so this could help you narrow down the field quite quickly.

6. Twitter – Does the site have a twitter page? If so try and spark up a conversation. Being active on Twitter is normally a sign that they are open and responsive to customer feedback.

All in all, these tips won’t take very long but will give you a good idea of one or two that you could try out, if not the exact reference manager you should use.

I will do my best to have a look through some of them and try to put some objective reviews up on the blog.











Jab Ref



The Links above are all absolutely FREE!! They won’t cost you a penny.

There are a few reference managers out there that you do have to pay for…





pdf Stack

Ref Works


Lab Meeting



  1. Paul says

    Mendeley is very smooth and low maintenance. I haven’t worked out how to use it for books but for viewing and organising PDF files it is superlative.

    Plus Mendeley has some iphone functionality, if that is what you’re after.

    • says

      Thanks for the info – I do like Mendeley. I don’t have an I phone yet but I can imaging it’s quite useful. I know people who use it on the ipad too.

  2. Rusty says

    I use RefWorks at no charge because my university library supports it. They also support Endnote and Zotero.  I would suggest that researchers always check to see what their university supports.

    • says

      Cool, RefWorks seems quite good. Wise words, ultimately you are responsible for submitting your work to the University and they are responsible to support you for certain things such as reference management. Institution support is very important so thanks for raising it.

  3. says

    I used EndNote at first, while still working with Word. That was such a hassle. Macro’s and other stuff didn’t work from the beginning, which meant lots of fiddling in Word. That was 8 years ago tho. Once I switched to LaTeX, my life got so much easier with respect to reference management. I just JabRef at first, which is a great but complex program. It specifically targets LaTeX, so I wouldn’t recommend it for a Word user.

    Half a year ago I searched for a new reference manager and tried Qiqqa and Mendeley. I also looked at Zotero, but that just worked with Firefox at that time. Since Qiqqa crashed on me, I used Mendeley.

    Mendeley does an excellent job at a few things:
    -import and recognize papers and others. Especially if you are using DOI’s, it’s an excellent piece of software.
    -filter and select papers based on tags, authors, keywords works pretty well. You can define your own tags and group papers by subject. It’s also possible to select all papers by author.
    -Synchronize between computers is a breeze, as it copies all papers (pdf’s in my case) to a central database online, which you can synchronize on multiple pc’s.

    One thing I would like Mendeley to improve is the search. Searching on multiple terms in all papers isn’t that easy. And once you’ve opened the PDF, you have to search again. It would be easier to have a better search. Besides, I don’t like the PDF viewer of Mendeley, so I tend to use the external (sumatraPDF). Mendeley is also not that excellent in the definition of LaTeX items for a bib file. Jabref is however an easy method to change the faulty ones (which I only use for final papers, not for drafts).

    Overall, I really recommend Mendeley, just for its reference management capabilities.

    • says

      Wow, another great comment. Thanks very much for sharing your insights. Do you use Mendeley exclusively now, or do you still use LaTeX as well?

  4. says

    Not sure why you have Bookends in your “free” list as eventually you will have to pay for it, the demo option limits the references (to 50 I think). The same with Mendeley, once you run out of the free space, you will have to pay for storage. 

    Mendeley crashed on my machine (iMac running Snow Leopard at the time) one too many times for it to work for me, so I had to abandon it, but I did like its interface and PDF annotation features. Bookends offers both database sync, and reference sharing, and looks like the one I will go with. RefWorks, as it is offered by my institution, is my “backup” storage area as it were. 

    I also looked at options that worked withScrivener , my text editor of choice, and that may be another aspect to consider. I use notations in my document that Bookends scans and replaces with the appropriate style. 

    • says

      You’re right with bookends sorry! I’ve changed it. With mendeley though, I’ve never paid for storage and used is a a fully functional reference manager in it’s own right which is why I list it as free. For free online pdf storage I use drop box and sugar sync which combined give you 10GB of free storage space which is enough for all my refs and then some!

      Do you use bookends now?

  5. HHkat says

    I prefer Mendeley as it is so much easier to use that most other ref managers ive used. its not perfect but the things i use a lot it does really well. also see 
    http://uclanprf.blogspot.co.uk/ for a decent review and some helpful links at the bottom to compare other ref managers

    • says

      I’ve really like Mendeley although Papers has impressed me recently. Thanks for the link to your blog.

  6. says

    As a mac user I wanted to use Endnote since it’s the only reference management software officially supported by my uni but at the time (about 3 years ago) there wasn’t a mac version. Fast forward to today and although I really enjoy using Mendeley I’m a convert of Sente which works like a treat for macs and iPads. The sync function between devices is ace and it’s very very easy to use since the layout is clean and simple (compared to Endnote). I’m taking a chance with using this software since, if I run into any issues with it and word I’m on my own in terms of uni support.

  7. GlassSpider says

    Hi, just found your site — terrific! Would have made getting organized for my dissertation much easier if I’d found it a couple years ago! I just wanted to chime in as another happy Mendeley user. It runs really smoothly on my mac and I love having all the pdfs of the papers easily accessible, organized into folders by subtopic.

    For me, it’s been much more than just a reference manager, it’s been a great tool for increasing the efficiency of my writing. I do a lit search, scan abstracts for relevance, and then download all articles I want into the Mendeley folder that matches the search terms. Then, when I sit down to read/organize and zero/first draft, I just open up a folder and all the pdfs in it, open a word doc, write a few general topic headings, and get going organizing key points with citations.

    The one point of gripe I have is that sometimes (especially with older pdfs), Mendeley sometimes really garbles the citation info, but it does flag these and ask you to verify, and it’s easy, if annoying, to edit and correct.


  1. […] 6 Tips on How to Choose Reference Management Software This article offers advice on choosing the right literature reference management software for your research. Selecting the right reference management software includes 1. Asking the people in your group what they use. 2. Having a look at the screen shots on the website of the individual reference manager. 3. Typing the name of the reference manager into You Tube to see how popular it is. 4. Using Google and seeing what kind of results you get back. 5. Asking “Is it compatible with your operating system?” 6. Twitter –Being active on twitter is normally a sign that they are open and responsive to customer feedback. (literaturereviewhq) […]