SISTR

SISTR (Salmonella In Silico Typing Resource) produces serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST.

Pathogenwatch uses the cgmlst_subspecies and serovar fields from the JSON output. https://hub.docker.com/r/ummidock/sistr_cmd is used as a base image.

How to cite

Yoshida CE, Kruczkiewicz P, Laing CR, et al. The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies. PLoS One. 2016;11(1):e0147101. Published 2016 Jan 22. doi:10.1371/journal.pone.0147101