Pathogenwatch
  • Welcome to Pathogenwatch
  • 🎉Announcements
  • ▶️A "Getting Started" Tutorial
  • 🎦Video Tutorials
  • 🧐Useful Links
  • 📖How to use Pathogenwatch
    • Uploading Genomes
    • Genome Reports
    • Browsing Genomes
    • Editing Metadata
    • 🚮Deleting genomes
    • Downloads
    • Creating A Collection
    • Browsing Collections
    • Sharing a collection
    • Genomic Context Search
    • Using The Interactive Collection Views
      • The Map View
      • The Tree Viewer
      • The Filter Bar
      • The Metadata Tables
        • Uploaded Metadata
        • Typing Results
        • Genome Statistics
        • Antimicrobial Resistance
    • Private Metadata
  • 📖Technical Descriptions
    • Species Assignment
      • Speciator
    • Sequence Typing Methods
      • cgMLST
      • Genotyphi
      • Kaptive
      • Kleborate
      • Klebsiella LIN Codes
      • MLST
      • NG-MAST
      • Pangolin
      • PopPUNK
      • SeroBA
      • Vista
      • SISTR
    • Antimicrobial Resistance Prediction
      • SPN-PBP-AMR
      • Kleborate
      • Pathogenwatch AMR
    • Inctyper
    • cgMLST Clustering
    • SARS-CoV-2 Notable Mutations
    • SARS-CoV-2 Genome Tree
    • Core Genome Tree
      • Core Assignment
      • Reference Assignment
      • Core Filter
      • Tree Construction
    • Short Read Assembly
  • ❓FAQ
  • 💾Public data downloads
  • 💊WHO bacterial priority pathogens
  • 📜Release Notes 2025
  • Release Notes 2024
  • Release Notes 2023
  • Release Notes 2022
  • Release Notes 2019-2021
  • ⚠️Privacy and Terms Of Service
  • 📣How to cite
  • 🙏Acknowledgements
  • ❗Report an Issue
Powered by GitBook
On this page
  1. Technical Descriptions
  2. Sequence Typing Methods

SISTR

PreviousVistaNextAntimicrobial Resistance Prediction

Last updated 10 months ago

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. 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

📖
https://hub.docker.com/r/ummidock/sistr_cmd