StaPH-B
[Repo Request]: add citation section to main README.md
What functionality is this repo missing?
This github repo is awesome, but...
We should add a "citation" section on the main README for the EID paper: https://wwwnc.cdc.gov/eid/article/31/13/24-1363_article
Perhaps we can say something along the lines of:
- We'd love a citation if you use these docker images, here's our paper: [https://wwwnc.cdc.gov/eid/article/31/13/24-1363_article](https://wwwnc.cdc.gov/eid/article/31/13/24-1363_article), and
- If you mention a bioinformatics tool specifically you should likely cite the tool's respective publication and/or code repository to give credit where it's due!
Also, need to look into the citation feature of GitHub. I think we would need to add a /citation.cff file and fill in the correct info: https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files
remove Authors/Maintainers section since github tracks contributors anyways: https://github.com/StaPH-B/docker-builds?tab=readme-ov-file#authorsmaintainers
I think the citation blurb could be something like the following
""" If you have found this resource useful please use the following citation in addition to the citations of the tools being used:
Florek KR, Young EL, Incekara K, Libuit KG, Kapsak CJ. Advantages of Software Containerization in Public Health Infectious Disease Genomic Surveillance. Emerg Infect Dis. 2025 May;31(13):18-21. doi: 10.3201/eid3113.241363. PMID: 40359055; PMCID: PMC12078543.
Hypothetical text example:
Reads were assembled with spades version 4.2.0 (PMID: 32559359) before AMR gene identification with AMRFinder version 4.0.23 database version 2025-06-03.1 (PMID: 34135355) using StaPH-B/docker-builds images (PMID: 40359055)
"""
FYI I started a dev branch for this. See here for the rendered version & the new "cite this repository" button which defaults to generating APA & BibTeX citations for the EID manuscript
https://github.com/StaPH-B/docker-builds/tree/cjk-citation