Acknowledgements
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
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
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