Publications
============

Citation
--------

When citing Pyrodigal, please additionally cite the original Prodigal paper,
which developed the actual method. You can for instance cite both papers as:
*Pyrodigal (Larralde, 2022), a Python library binding to Prodigal (Hyatt et al., 2010).*

Use the following for the bibliography:

- `Hyatt, D., Chen, GL., LoCascio, P.F. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010). doi:10.1186/1471-2105-11-119 <https://doi.org/10.1186/1471-2105-11-119>`_.
- `Larralde, M., (2022). Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes. Journal of Open Source Software, 7(72), 4296. doi:10.21105/joss.04296 <https://doi.org/10.21105/joss.04296>`_.

Or just grab the `BibTex file <_static/bibtex/citation.bib>`_ with these two papers.


JOSS
----

Pyrodigal has been published in the `Journal of Open-Source Science <https://joss.theoj.org>`_.
JOSS is a community-run journal and relies upon volunteer effort. If you'd like
to support JOSS please consider doing either one (or both) of the the following:

- Volunteering to review for JOSS sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html.
- Making a small donation to support running costs here: https://numfocus.org/donate-to-joss.


Users
-----

Pyrodigal is being used in the following research works:

- `Carroll, L. M., Larralde, M., Fleck, J. S., Ponnudurai, R., Milanese, A., Cappio, E., Zeller, G.  Accurate de novo identification of biosynthetic gene clusters with GECCO. bioRxiv 2021.05.03.442509; doi:10.1101/2021.05.03.442509 <https://doi.org/10.1101/2021.05.03.442509>`_.
- `Santos-Júnior C.D., Pan, S., Zhao, X., Coelho, L.P.  Macrel: antimicrobial peptide screening in genomes and metagenomes. PeerJ 8:e10555. doi:10.7717/peerj.10555 <https://doi.org/10.7717/peerj.10555>`_.
- `Sirén K., Millard, A., Petersen, B., Gilbert, M. T. P., Clokie, M. RJ., Sicheritz-Pontén, T. Rapid discovery of novel prophages using biological feature engineering and machine learning. bioRxiv 2020.08.09.243022; doi:10.1101/2020.08.09.243022 <https://doi.org/10.1101/2020.08.09.243022>`_.
- `Turkington, C. J. R., Nezam Abadi, N., Edwards, R. A., Grasis, J. A.  hafeZ: Active prophage identification through read mapping. bioRxiv 2021.07.21.453177; doi:10.1101/2021.07.21.453177  <https://doi.org/10.1101/2021.07.21.453177>`_.
- `Reynolds, R., Hyun, S., Tully, B., Bien, J., Levine, N. M. Identification of microbial metabolic functional guilds from large genomic datasets. Front Microbiol. 2023 Jun 30;14:1197329. doi:10.3389/fmicb.2023.1197329. <https://doi.org/10.3389/fmicb.2023.1197329>`_.

Feel free to get in touch to add yours to the list!