# Pathogenwatch Documentation

## Pathogenwatch 

- [Welcome to Pathogenwatch](https://cgps.gitbook.io/pathogenwatch/readme.md): Pathogenwatch provides a platform for comparing pathogen genomes from around the world, integrating diverse data sets with rich representations.
- [News & Release Notes](https://cgps.gitbook.io/pathogenwatch/news-and-release-notes.md)
- [Announcements](https://cgps.gitbook.io/pathogenwatch/news-and-release-notes/announcements.md)
- [Release Notes 2026](https://cgps.gitbook.io/pathogenwatch/news-and-release-notes/release-notes-2026.md): Pathogenwatch release notes for 2026
- [Release Notes 2025](https://cgps.gitbook.io/pathogenwatch/news-and-release-notes/release-notes-2025.md): Pathogenwatch Release Notes for 2025.
- [Release Notes 2024](https://cgps.gitbook.io/pathogenwatch/news-and-release-notes/release-notes-2024.md): Pathogenwatch release notes for 2024
- [Release Notes 2023](https://cgps.gitbook.io/pathogenwatch/news-and-release-notes/release-notes-2023.md): Pathogenwatch release notes for 2023
- [Release Notes 2022](https://cgps.gitbook.io/pathogenwatch/news-and-release-notes/release-notes-2022.md): Pathogenwatch release notes for 2022
- [Release Notes 2019-2021](https://cgps.gitbook.io/pathogenwatch/news-and-release-notes/release-notes-2019-2021.md): View descriptions of the updates and fixes in each release from 2021 or before
- [Getting Started](https://cgps.gitbook.io/pathogenwatch/getting-started.md)
- [Sign in](https://cgps.gitbook.io/pathogenwatch/getting-started/sign-in.md)
- [A Brief Tour of Pathogenwatch](https://cgps.gitbook.io/pathogenwatch/getting-started/a-brief-tour-of-pathogenwatch.md)
- [Interactive Collection View tutorial](https://cgps.gitbook.io/pathogenwatch/getting-started/interactive-collection-view-tutorial.md): A short walkthrough of several features of the Interactive Collection View.
- [SARS-CoV-2 Tutorial](https://cgps.gitbook.io/pathogenwatch/getting-started/sars-cov-2-tutorial.md)
- [Useful Links](https://cgps.gitbook.io/pathogenwatch/getting-started/useful-links.md)
- [How to use Pathogenwatch](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch.md)
- [Using the documentation](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/using-the-documentation.md)
- [Uploads and Projects](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/uploads-and-folders.md)
- [Genome Uploads & Projects](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/uploads-and-folders/genome-uploads-folders.md): Description of the Upload page, file formats, and Projects page.
- [Projects](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/uploads-and-folders/folders.md): How to use the Pathogenwatch projects to manage your genomes
- [Browsing and Viewing Genomes](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes.md)
- [Browsing & Searching Genomes](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/browsing-searching-genomes.md)
- [Viewing Genome Reports](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/genome-reports.md): Detailed reports on individual genomes.
- [Editing metadata](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/editing-metadata.md): How to edit the metadata of your genomes after upload
- [Collections](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections.md)
- [Using The Interactive Collection View](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv.md)
- [The Interactive Collection View](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/the-interactive-collection-view.md)
- [The Collection Header](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/the-collection-header.md): The header provides access to collection information, search and other utilities.
- [The Map Panel](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/map-panel.md)
- [The Tree Panel](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/tree-panel.md)
- [Tree Panel](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/tree-panel/tree-panel.md)
- [Generating a new tree](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/tree-panel/generating-a-new-tree.md)
- [Data Tables](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/data-tables.md)
- [The Timeline Panel](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/timeline.md)
- [Context search panel](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/context-search.md)
- [Legend, Labels, and Colours](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/legend-labels-and-colours.md)
- [Searching genomes in a collection](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/searching-genomes-in-a-collection.md)
- [Integrating private metadata](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/integrating-private-metadata.md): The collection viewer allows local-only analysis of confidential metadata
- [Creating sub-collections](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/creating-sub-collections.md)
- [Creating & Sharing Collections](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/creating-sharing-collections.md)
- [Browsing Collections](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/browsing-collections.md)
- [Genomic Neighbourhood Search](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/genomic-neighbourhood-search.md): The Pathogenwatch context search service
- [Context search overview](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/genomic-neighbourhood-search/context-search-overview.md): The basic of how the search tool works
- [Single genome seach](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/genomic-neighbourhood-search/single-genome-seach.md): How to generate a context for a single genome
- [Collection search](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/genomic-neighbourhood-search/collection-search.md): Exploring the genomic neighbourhood for a collection of genomes
- [The cluster viewer](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/genomic-neighbourhood-search/the-cluster-viewer.md): How to use the interactive cluster viewer
- [Downloading Data](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/downloading-data.md): How to download FASTAs, metadata and analysis results from Pathogenwatch
- [Deleting items](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/deleting-items.md)
- [Tips and Tricks](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/tips-and-tricks.md): Please contact us if you have Tips & Tricks to add to this page
- [The API](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/the-api.md): Programmatic access to Pathogenwatch
- [Technical Descriptions of Analysis Tools](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools.md)
- [Genome Assembly](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/genome-assembly.md)
- [Short Read Assembly](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/genome-assembly/short-read-assembly.md): How Pathogenwatch assembles short read Illumina data
- [Assigning species with Speciator](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/speciator.md): Species assignment tool in Pathogenwatch
- [Assembly QC](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/assembly-qc.md)
- [Lineage Assignment & Genotyping Methods](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping.md)
- [cgMLST](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/cgmlst.md)
- [Genotyphi](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/genotyphi.md)
- [Geno7PET](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/geno7pet.md): Sublineage assignments for Vibrio cholerae 7PET pandemic strains
- [HierCC](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/finding-hiercc-codes-with-hclink.md): Linking Enterobase HierCC clusters using the hclink software
- [Kleborate](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/kleborate.md): Klebsiella comprehensive AMR and typing analysis software.
- [Klebsiella LIN Codes](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/klebsiella-lin-codes.md): The Pathogenwatch LIN code tool infers Klebsiella lineage codes based on references from the Pasteur/PubMLST resource.
- [MLST](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/mlst.md)
- [NG-MAST](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/ng-mast.md)
- [NG-STAR](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/ng-star.md): Resistance-based typing of Neisseria gonorrhoeae
- [Pangolin](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/pangolin.md): SARS-CoV-2 lineage assignment tool
- [PopPUNK](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/poppunk.md): S. pneumoniae GPSC strain assignment
- [SARS-CoV-2 Notable Mutations](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/sars-cov-2-notable-mutations.md): Identification of mutations described in the Type Variants database
- [Vista](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/vista.md): Virulence and genotype annotation tool for Vibio cholerae
- [Antimicrobial Resistance Prediction](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/antimicrobial-resistance-prediction.md): Links to the documentation for the AMR tools in Pathogenwatch and currently annotated species.
- [Pathogenwatch AMR](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/antimicrobial-resistance-prediction/pw-amr.md): The Pathogenwatch AMR prediction library and pipeline.
- [Kleborate AMR](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/antimicrobial-resistance-prediction/kleborate.md)
- [SPN-PBP-AMR](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/antimicrobial-resistance-prediction/spn-pbp-amr.md): Analysis of the Streptococcus pneumoniae PBPs and inferred MICs.
- [Resfinder](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/antimicrobial-resistance-prediction/resfinder.md): About the Resfinder software and integration in Pathogenwatch
- [Trees, Clustering, and Context Search](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search.md)
- [Core Genome Tree](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree.md)
- [About SNP-based trees](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree/about-snp-based-trees.md)
- [Core Assignment](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree/core-assignment.md)
- [Core Filter](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree/core-filter.md)
- [Reference Assignment](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree/reference-assignment.md)
- [Tree Construction](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree/tree-construction.md)
- [cgMLST Clustering & Context Searching](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/cgmlst-clustering.md)
- [SARS-CoV-2 Genome Tree](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/sars-cov-2-genome-tree.md): How SARS-CoV-2 trees are constructed in Pathogenwatch.
- [cgMLST Tree](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/cgmlst-tree.md): How cgMLST profile-based trees are constructed
- [Serotyping](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/serotyping.md)
- [Kaptive](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/serotyping/kaptive.md): A tool for typing the surface polysaccharide loci of Klebsiella and A. baumanii
- [SeroBA](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/serotyping/seroba.md)
- [SISTR](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/serotyping/sistr.md)
- [ECTyper](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/serotyping/ectyper.md): About the ECTyper serotyping tool
- [Virulence](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/virulence.md): Virulence annotation tools in Pathogenwatch.
- [STECFinder](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/virulence/stecfinder.md): Shiga toxin genotyping
- [VirulenceFinder](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/virulence/virulencefinder.md): Virulence gene annotation
- [BIGSdb schemes](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/virulence/bigsdb-schemes.md): Pathogenwatch supports integrating virulence schemes from BigsDB
- [Plasmid Annotation](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/plasmid-annotation.md)
- [Plasmidfinder](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/plasmid-annotation/plasmidfinder.md): Identification and typing of plasmid replicons in whole-genome sequencing (WGS).
- [Change log](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/change-log.md)
- [The Real Time Assembly Pipeline](https://cgps.gitbook.io/pathogenwatch/the-real-time-assembly-pipeline.md): Always on pipeline generating public data sets for key pathogens
- [Supported Organisms](https://cgps.gitbook.io/pathogenwatch/supported-organisms.md): Pathogenwatch focus species
- [WHO bacterial priority pathogens](https://cgps.gitbook.io/pathogenwatch/old-who-bacterial-priority-pathogens.md): AMR annotation coverage of the WHO priority pathogens for AMR research and control by Pathogenwatch.
- [How to cite](https://cgps.gitbook.io/pathogenwatch/how-to-cite.md): How to cite Pathogenwatch and the analysis tools
- [Acknowledgements](https://cgps.gitbook.io/pathogenwatch/acknowledgements.md): Resources, funding and hosting of Pathogenwatch
- [Privacy and Terms Of Service](https://cgps.gitbook.io/pathogenwatch/privacy-and-tos.md)
- [FAQ](https://cgps.gitbook.io/pathogenwatch/faq.md): Frequently asked questions and other tips for using Pathogenwatch.
- [Report an Issue](https://cgps.gitbook.io/pathogenwatch/report-an-issue.md): Website crash, data error, documentation or feature request.

## PATH-SAFE

- [The National Foodborne Genomic Data platform documentation](https://cgps.gitbook.io/pathogenwatch/path-safe/readme.md): Documenting PATH-SAFE on Pathogenwatch and CLIMB
- [Getting an account](https://cgps.gitbook.io/pathogenwatch/path-safe/getting-an-account.md): Onboarding and account creation
- [Common workflows](https://cgps.gitbook.io/pathogenwatch/path-safe/common-workflows.md): A few standard workflows supported for PATH-SAFE
- [Uploading genomes](https://cgps.gitbook.io/pathogenwatch/path-safe/uploading-genomes.md): Via CLIMB
- [What is the Food Surveillance Programme?](https://cgps.gitbook.io/pathogenwatch/path-safe/what-is-the-path-safe-programme.md): Enabling data sharing for One Health surveillance of foodborne pathogens
- [PATH-SAFE Sign in](https://cgps.gitbook.io/pathogenwatch/path-safe/pathogenwatch/signing-in.md): Using the CLIMB secure OAuth service
- [PATH-SAFE powered by Pathogenwatch](https://cgps.gitbook.io/pathogenwatch/path-safe/pathogenwatch/path-safe-powered-by-pathogenwatch.md)
- [PATH-SAFE analyses](https://cgps.gitbook.io/pathogenwatch/path-safe/pathogenwatch/path-safe-analyses.md): Analyses specifically evaluated and validated for the PATH-SAFE programme
- [PATH-SAFE genome assembly with EToKI](https://cgps.gitbook.io/pathogenwatch/path-safe/pathogenwatch/genome-assembly.md): Specialised assembly pipeline available to the PATH-SAFE Initiative
- [Two-tool Serotyping with SISTR & SeqSero2](https://cgps.gitbook.io/pathogenwatch/path-safe/pathogenwatch/two-tool-serotyping-with-sistr-and-seqsero2.md): This two-tool serotyping method is available to some initiatives (e.g. PATH-SAFE)
- [S. enterica SNP tree](https://cgps.gitbook.io/pathogenwatch/path-safe/pathogenwatch/salmonella-enterica-scheme.md): Developing the SNP tree method