Question: How do you cite a tool that doesn't have a publication?
gravatar for novice
20 months ago by
United States
novice710 wrote:

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

citation academic style • 9.1k views
ADD COMMENTlink modified 19 months ago by Emily_Ensembl13k • written 20 months ago by novice710
gravatar for Bioaln
20 months ago by
Bioaln230 wrote:

I suggest you use the author, date and link.

ADD COMMENTlink written 20 months ago by Bioaln230

How does this look?

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

ADD REPLYlink written 20 months ago by novice710

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

ADD REPLYlink written 20 months ago by Ram12k
gravatar for Emily_Ensembl
19 months ago by
Emily_Ensembl13k 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 From our investigations, we've found that over 2/3 of the papers that mention Ensembl do not cite our papers.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 19 months ago by Emily_Ensembl13k

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 19 months ago by Ibrahim Tanyalcin820

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 19 months ago • written 19 months ago by Emily_Ensembl13k

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 19 months ago by John12k

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 19 months ago by novice710

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 8 months ago by timdemeyerugent0
gravatar for genomax
20 months ago by
United States
genomax37k 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 20 months ago • written 20 months ago by genomax37k
gravatar for Ibrahim Tanyalcin
20 months ago by
Ibrahim Tanyalcin820 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 8 months ago by Ram12k • written 20 months ago by Ibrahim Tanyalcin820
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