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7. Citation
If you found the BTyper3 tool, its source code, and/or any of its associated databases useful, please cite:
Carroll, Laura M., Martin Wiedmann, Jasna Kovac. 2020. "Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes." mBio 11(1): e00034-20; DOI: 10.1128/mBio.00034-20.
Carroll, Laura M., Rachel A. Cheng, Jasna Kovac. 2020. "No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus group with Historical Typing Methods." Frontiers in Microbiology 11: 580691; DOI: 10.3389/fmicb.2020.580691.
If you used BTyper3 to perform species and/or subspecies and/or pseudo-gene flow unit assignment, please additionally cite:
Jain, Chirag, Luis M. Rodriguez-R, Adam M. Phillippy, Konstantinos T. Konstantinidis, Srinivas Aluru. 2018. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nature Communications 9(1):5114. doi: 10.1038/s41467-018-07641-9.
If you used BTyper3 to perform biovar assignment and/or to identify virulence factors and/or to identify Bt toxin-encoding genes and/or to perform in silico MLST and/or panC group assignment, please additionally cite:
Camacho, Christiam, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10:421. doi: 10.1186/1471-2105-10-421.
Cock, Peter J. A., Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon. 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11): 1422–1423. doi: 10.1093/bioinformatics/btp163.
If you used BTyper3 to perform seven-gene MLST, please additionally cite:
Jolley, Keith A., James E. Bray, Martin C.J. Maiden. 2018. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Research 3: 124. doi: doi:10.12688/wellcomeopenres.14826.1
Disclaimer: BTyper3 is pretty neat! However, no tool is perfect, and BTyper3 cannot definitively prove whether an isolate is pathogenic or not. As always, interpret your results with caution. We are not responsible for taxonomic misclassifications, misclassifications of an isolate's pathogenic potential or industrial utility, and/or misinterpretations (biological, statistical, or otherwise) of BTyper3 results.