> For the complete documentation index, see [llms.txt](https://cgps.gitbook.io/pathogenwatch/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/serotyping/sistr.md).

# 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