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
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Technical Descriptions

PreviousPrivate MetadataNextSpecies Assignment

Last updated 3 years ago

📖
Species Assignment
Sequence Typing Methods
Antimicrobial Resistance Prediction
Inctyper
cgMLST Clustering
SARS-CoV-2 Notable Mutations
SARS-CoV-2 Genome Tree
Core Genome Tree
Short Read Assembly