next.pathogen.watch docs
  • Welcome to Pathogenwatch
  • News & Release Notes
    • Announcements
    • Release Notes 2025
    • Release Notes 2024
    • Release Notes 2023
    • Release Notes 2022
    • Release Notes 2019-2021
  • Getting Started
    • Sign in
    • A Brief Tour of Pathogenwatch
    • Interactive Collection View tutorial
    • Useful Links
  • How to use Pathogenwatch
    • Using the documentation
    • Using The Interactive Collection View
      • The Interactive Collection View
      • The Map Panel
      • The Tree Panel
        • Tree Panel
        • Generating a new tree
      • Data Tables
      • The Timeline Panel
      • Context search panel
      • Legend, Labels, and Colours
      • Searching genomes in a collection
      • Creating sub-collections
    • Genome Uploads & Folders
    • Browsing & Searching Genomes
    • Browsing Collections
    • Creating & Sharing Collections
    • Genome Reports
    • Deleting items
    • SARS-CoV-2 Tutorial
    • Tips and Tricks
  • Technical Descriptions of Analysis Tools
    • Genome Assembly
      • Short Read Assembly
      • Assembling genomes with EToKi
    • Plasmid Annotation
      • Inctyper
    • Assigning species with Speciator
    • Trees, Clustering, and Context Search
      • Core Genome Tree
        • About SNP-based trees
        • Core Assignment
        • Core Filter
        • Reference Assignment
        • Tree Construction
      • cgMLST Clustering & Context Searching
      • SARS-CoV-2 Genome Tree
      • cgMLST Tree
    • Lineage Assignment & Genotyping Methods
      • Genotyphi
      • Kleborate
      • cgMLST
      • Klebsiella LIN Codes
      • MLST
      • NG-MAST
      • Pangolin
      • PopPUNK
      • Vista
      • Finding HierCC codes with hclink
      • SARS-CoV-2 Notable Mutations
    • Serotyping
      • Kaptive
      • SeroBA
      • SISTR
      • ECTyper
    • Antimicrobial Resistance Prediction
      • Pathogenwatch AMR
      • Kleborate AMR
      • SPN-PBP-AMR
      • Resfinder
    • Virulence
      • STECFinder
      • VirulenceFinder
      • BIGSdb schemes
  • WHO bacterial priority pathogens
  • Initiatives powered by Pathogenwatch
    • PATH-SAFE
      • PATH-SAFE Sign in
      • What is the PATH-SAFE Programme?
      • PATH-SAFE powered by Pathogenwatch
      • Two-tool Serotyping with SISTR & SeqSero2
      • S. enterica SNP tree
      • PATH-SAFE analyses
  • How to cite
  • Acknowledgements
  • Privacy and Terms Of Service
  • FAQ
  • Report an Issue
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