Question: How do you cite a tool that doesn't have a publication?
gravatar for novice
4.0 years ago by
United States
novice950 wrote:

FASTQC, for example, doesn't seem to have a publication associated with it. How would you cite it?

citation academic style • 25k views
ADD COMMENTlink modified 3.8 years ago by Emily_Ensembl20k • written 4.0 years ago by novice950
gravatar for Bioaln
4.0 years ago by
Bioaln340 wrote:

I suggest you use the author, date and link.

ADD COMMENTlink written 4.0 years ago by Bioaln340

How does this look?

Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at:

ADD REPLYlink written 4.0 years ago by novice950

If anyone is looking for bibtex. Here you go,

  address = {{Babraham, UK}},
  title = {{{FastQC}}},
  copyright = {GPL v3},
  abstract = {FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.},
  howpublished = {Babraham Institute},
  author = {Andrews, Simon and Krueger, Felix and {Segonds-Pichon}, Anne and Biggins, Laura and Krueger, Christel and Wingett, Steven},
  month = jan,
  year = {2012}
ADD REPLYlink written 7 months ago by Dexter20

Why would that reference be 2012 and not 2010? Are you considering the version of the software used in the article to be put into the citation?

ADD REPLYlink written 4 weeks ago by beausoleilmo300

Exactly - I've seen links used to cite blog posts; they should be useful for tools too.

ADD REPLYlink written 4.0 years ago by RamRS25k
gravatar for Emily_Ensembl
3.8 years ago by
Emily_Ensembl20k wrote:

Just to say, thank you for wanting to cite tools. From our investigations, we've found that over 2/3 of the papers that mention Ensembl do not cite our papers. No idea how many more than that use our stuff and don't even bother to mention us. It's as if people think that building a bioinformatic database or tool is not real science, so doesn't need acknowledgement. In science, citations are currency, and using someone's work without citing them is essentially theft.

ADD COMMENTlink written 3.8 years ago by Emily_Ensembl20k

2/3rds of my wetlab work never resulted in authorship either, and just like writing a tool i'm talking about months of work. It's certainly a lot easier to use FastQC or Ensembl datasets without acknowledgement than a BSc/Masters/PhD student -- particularly it if there's no 'proof' of usage in the paper ("The quality of our data... ...looked good based on a variety of metrics / ...compared favorably to other publicly available datasets.") -- however, I think it must have been Socrates who once said: "Don't hate the player, hate the game". More and more these days Science appears to be a 0-sum game - particularly to young scientists who after their PhD have only a 1 in 200 chance of becoming an independent researcher. Under those conditions, a mentality of "take as much credit as possible, and only hand it out where absolutely necessary" is an inevitability. I wish we could go back to the old-days, but I think it's more realistic that tool/service developers forget about asking nicely for people to do the right thing, and instead think of ways to ensure citations where tools where used and punishments if they don't. Alternatively, research like yours showing the disparity between use and citations needs to be done to really make it known how valuable services like Ensembl are to life sciences.

ADD REPLYlink written 3.8 years ago by John12k

Great point. However the reviewers of journals can also comment on the references. In principle they can use this power to enforce everyone to give proper credit. Is it the case? I don't know. So researchers are just part of the whole story..

ADD REPLYlink written 3.8 years ago by Ibrahim Tanyalcin1.0k

But if 2/3 of the people writing papers think they don't need to cite databases or tools, then a similar 2/3 of reviewers probably have the same attitude. Or maybe 80% of both groups think you don't need to cite, and only by the small number of referees who think it's important pointing it out do we get the citation rate as high as 1/3.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Emily_Ensembl20k

Thank you for providing tools for all of us! I have nothing but respect for the people behind good, open source software.

ADD REPLYlink written 3.8 years ago by novice950

Note that journals often restrict the number of references included in the manuscript, making the "standard" tools/databases/repositories such as Ensembl the first victim.

ADD REPLYlink written 2.9 years ago by timdemeyerugent10

I keep telling people this because having the citations also assists others in reproducing analyses. Unfortunately, many journal editors and reviewers don't want to know about the bioinformatics methodologies and, thus, this information is frequently overlooked in published work.

ADD REPLYlink written 2.0 years ago by Kevin Blighe54k
gravatar for genomax
4.0 years ago by
United States
genomax78k wrote:

You would cite the web link for the tool. Simon (author of FastQC) had suggested that in the past for FastQC.

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by genomax78k
gravatar for Ibrahim Tanyalcin
4.0 years ago by
Ibrahim Tanyalcin1.0k wrote:

I would also try to include the DOI into the citation. If the software is in biorxiv, it will already get a doi, else if the software is in Github, the owner of the repository can also acquire one from zenodo (

ADD COMMENTlink modified 2.9 years ago by RamRS25k • written 4.0 years ago by Ibrahim Tanyalcin1.0k
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