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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  1. How to use Pathogenwatch

Genome Reports

Detailed reports on individual assemblies.

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Last updated 4 years ago

Genome Reports

A detailed report on each assembly can be accessed from the Genome tab or from within the Cluster or Collection views by clicking on the assembly name. The assembly report includes detailed results for each tool run by Pathogenwatch, e.g. MLST or Genotyphi, along with metadata and assembly metrics such as N50. The version of each tool is also tagged, and a link to the original FASTA provided at the top.

Clicking the printer icon in the corner will generate a printable version of the report.

Core genome-based neighbourhood searches

From here the cgMLST-based clusters can also be accessed. For species where a cgMLST scheme exists, a "Clusters" section will appear in the report. Pressing the "Cluster Now" button will search for near-neighbours within both yours and any public genomes and create a set of single-linkage clusters according to the specified cgMLST allele similarity threshold. For details see the . Clicking the link next to a cluster will allow you to view the cluster as a .

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cgMLST-Clusters description
Collection View