🙏Acknowledgements

Databases

http://bigsdb.pasteur.fr/

https://cgmlst.org

http://enterobase.warwick.ac.uk/ Alikhan et al. (2018) PLoS Genet 14 (4): e1007261

https://www.ncbi.nlm.nih.gov/refseq/

https://pubmlst.org

Tools and Methods

BLAST - https://blast.ncbi.nlm.nih.gov

Genotyphi - https://github.com/katholt/genotyphi An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. Wong VK, Baker S, Connor TR, Pickard D, Page AJ, Dave J, Murphy N, Holliman R, Sefton A, Millar M, Dyson ZA, Dougan G, Holt KE, International Typhoid Consortium. https://doi.org/10.1038/ncomms12827

Kleborate - https://github.com/katholt/Kleborate

Mash - https://github.com/marbl/mash Mash: fast genome and metagenome distance estimation using MinHash. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. https://doi.org/10.1186/s13059-016-0997-x

ngmaster - https://github.com/MDU-PHL/ngmaster In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST). Kwong JC, Gonçalves da Silva A, Dyet K, Williamson DA, Stinear TP, Howden BP and Seemann T. https://doi.org/10.1099/mgen.0.000076

PopPUNK - https://github.com/johnlees/PopPUNK Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW, Weiser JN, Corander J, Bentley SD, Croucher NJ. Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome Research 29:304-316 (2019). doi:10.1101/gr.241455.118

SeroBA - https://github.com/sanger-pathogens/seroba SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data Epping L, van Tonder, AJ, Gladstone RA, GPS Consortium, Bentley SD, Page AJ, Keane JA, Microbial Genomics 2018, doi: 10.1099/mgen.0.000186

SISTR - https://github.com/phac-nml/sistr_cmd The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada. PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147101