Citation

George Bouras, Roshan Nepal, Ghais Houtak, Alkis James Psaltis, Peter-John Wormald, Sarah Vreugde, Pharokka: a fast scalable bacteriophage annotation tool, Bioinformatics, Volume 39, Issue 1, January 2023, btac776, https://doi.org/10.1093/bioinformatics/btac776

If you use pharokka, I would recommend a citation in your manuscript along the lines of:

  • All phages were annotated with Pharokka v ___ (Bouras, et al. 2023). Specifically, coding sequences (CDS) were predicted with PHANOTATE (McNair, et al. 2019), tRNAs were predicted with tRNAscan-SE 2.0 (Chan, et al. 2021), tmRNAs were predicted with Aragorn (Laslett, et al. 2004) and CRISPRs were preducted with CRT (Bland, et al. 2007). Functional annotation was generated by matching each CDS to the PHROGs (Terzian, et al. 2021), VFDB (Chen, et al. 2005) and CARD (Alcock, et al. 2020) databases using MMseqs2 (Steinegger, et al. 2017) and PyHMMER (Larralde and Zeller 2023). Contigs were matched to their closest hit in the INPHARED database (Cook, et al. 2021) using mash (Ondov, et al. 2016). Plots were created with pyCirclize (Shimoyama 2022).

With the following full citations for the constituent tools below where relevant:

  • Cook R, Brown N, Redgwell T, Rihtman B, Barnes M, Clokie M, Stekel DJ, Hobman JL, Jones MA, Millard A. INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes. PHAGE. 2021. Available from: http://doi.org/10.1089/phage.2021.0007.
  • McNair K., Zhou C., Dinsdale E.A., Souza B., Edwards R.A. (2019) "PHANOTATE: a novel approach to gene identification in phage genomes", Bioinformatics, https://doi.org/10.1093/bioinformatics/btz26.
  • Chan, P.P., Lin, B.Y., Mak, A.J. and Lowe, T.M. (2021) "tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes", Nucleic Acids Res., https://doi.org/10.1093/nar/gkab688.
  • Steinegger M. and Soeding J. (2017), "MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets", Nature Biotechnology https://doi.org/10.1038/nbt.3988.
  • Ondov, B.D., Treangen, T.J., Melsted, P. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 17, 132 (2016). https://doi.org/10.1186/s13059-016-0997-x.
  • Terzian P., Olo Ndela E., Galiez C., Lossouarn J., Pérez Bucio R.E., Mom R., Toussaint A., Petit M.A., Enault F., "PHROG : families of prokaryotic virus proteins clustered using remote homology", NAR Genomics and Bioinformatics, (2021), https://doi.org/10.1093/nargab/lqab067.
  • Bland C., Ramsey L., Sabree F., Lowe M., Brown K., Kyrpides N.C., Hugenholtz P. , "CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats", BMC Bioinformatics, (2007), https://doi.org/10.1186/1471-2105-8-209.
  • Laslett D., Canback B., "ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.", Nucleic Acids Research (2004) https://doi.org/10.1093/nar/gkh152.
  • Chen L., Yang J., Yao Z., Sun L., Shen Y., Jin Q., "VFDB: a reference database for bacterial virulence factors", Nucleic Acids Research (2005) https://doi.org/10.1093/nar/gki008.
  • Alcock et al, "CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database." Nucleic Acids Research (2020) https://doi.org/10.1093/nar/gkz935.
  • 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.
  • Larralde M., Zeller G., (2023). PyHMMER: a Python library binding to HMMER for efficient sequence analysis, Bioinformatics, Volume 39, Issue 5, May 2023, btad214, https://doi.org/10.1093/bioinformatics/btad214.
  • Larralde M. and Camargo A., (2023) Pyrodigal-gv: A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code. https://github.com/althonos/pyrodigal-gv.
  • Shimoyama, Y. (2022). pyCirclize: Circular visualization in Python [Computer software]. https://github.com/moshi4/pyCirclize