Serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST. Mash MinHash can also be used for serovar prediction.
sistr_cmd on Github: https://github.com/peterk87/sistr_cmd
Don’t want to use a command-line app? Try the SISTR web app
If you find this tool useful, please cite as:
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
You can install sistr_cmd using pip
If you encounter any problems or have any questions feel free to create an issue anonymously or not to let us know so we can address it!
Copyright 2016 Public Health Agency of Canada
Distributed under the GNU Public License version 3.0
TODO: Figure out how to actually get changelog content.
Changelog content for this version goes here.