Pathogenwatch
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  • Welcome to Pathogenwatch
  • ๐ŸŽ‰Announcements
  • โ–ถ๏ธA "Getting Started" Tutorial
  • ๐ŸŽฆVideo Tutorials
  • ๐ŸงUseful Links
  • ๐Ÿ“–How to use Pathogenwatch
    • Uploading Genomes
    • Genome Reports
    • Browsing Genomes
    • Editing Metadata
    • ๐ŸšฎDeleting 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
  • ๐Ÿ“–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
  • โ“FAQ
  • ๐Ÿ’พPublic data downloads
  • ๐Ÿ’ŠWHO bacterial priority pathogens
  • ๐Ÿ“œRelease Notes 2025
  • Release Notes 2024
  • Release Notes 2023
  • Release Notes 2022
  • Release Notes 2019-2021
  • โš ๏ธPrivacy and Terms Of Service
  • ๐Ÿ“ฃHow to cite
  • ๐Ÿ™Acknowledgements
  • โ—Report an Issue
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  1. ๐Ÿ“–Technical Descriptions

Species Assignment

Pathogenwatch species assignments are generated using Speciator.

Speciator

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Last updated 1 year ago