# 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 Folders](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/uploads-and-folders.md) - [Genome Uploads & Folders](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/uploads-and-folders/genome-uploads-folders.md): Description of the Upload page, file formats, and Folders page. - [Folders](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/uploads-and-folders/folders.md): How to use the Pathogenwatch folders 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) - [Genotyphi](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/genotyphi.md) - [Kleborate](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/kleborate.md): Klebsiella comprehensive AMR and typing analysis software. - [cgMLST](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/cgmlst.md) - [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 - [Vista](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/vista.md): Virulence and genotype annotation tool for Vibio cholerae - [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 - [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 - [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 --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on a page URL with the `ask` query parameter: ``` GET https://cgps.gitbook.io/pathogenwatch/readme.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.