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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  • My Collections
  • Shared Collections
  • Public Collections
  1. How to use Pathogenwatch

Browsing Collections

PreviousBrowsing & Searching GenomesNextCreating & Sharing Collections

Last updated 5 months ago

The Collections page is accessible from the "Collections" and "Browse Collections" menu items. This page shows all collections available to you, shown as cards in three categories:

  • "" - owned by you

  • "" - owned by other users and shared specifically with you

  • "" - owned by the Pathogenwatch team and visible to everyone

A Search bar helps you find specific collections by name.

This page is where you can owned by you.

My Collections

If you are signed in, the collections you own will be listed here. You can these with other users or delete them.

Shared Collections

If you are signed in, this section will display any collections that have been shared specifically with you by their owners. Your permissions may vary, depending on whether you were invited as a "Viewer," "Editor," or "Manager" by the collections' owners.

Public Collections

Pathogenwatch provides pre-generated collections of publicly available genomes from important papers, surveys and in-house collections. These can be studied directly, and often represent the easiest way to use and download sequence and metadata associated with publications. You can also merge these collections with other sets of genomes, including your own downloads, via the page.

My Collections
Shared Collections
Public Collections
delete collections
share
Genomes