FASTQC, for example, doesn't seem to have a publication associated with it. How would you cite it?
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 From our investigations, we've found that over 2/3 of the papers that mention Ensembl do not cite our papers.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.