> For the complete documentation index, see [llms.txt](https://cgps.gitbook.io/pathogenwatch/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cgps.gitbook.io/pathogenwatch/supported-organisms.md).

# Supported Organisms

## About

Pathogenwatch provides annotation pipelines for a limited set of species. The pipelines for these species have been constructed and validated with community experts to provide robust, reliable results, and [assembly QC parameters](/pathogenwatch/technical-descriptions-of-analysis-tools/assembly-qc.md) are provided for each one.

## Species Selection

The selected species have chosen through a combination of important to public health as indicated by inclusion in the WHO priority pathogens (e.g. *Enterobacter cloacae* complex), or public health burden (e.g. *Vibrio cholerae* or SARS-CoV-2). In some cases, the support is also for historical project reasons (e.g. *Candida auris*), or for use as a type species in developing our internal tools (e.g. *Renibacterium salmoninarum*).

We are happy to consider new species of public health importance, provided they meet the following criteria:

* Significant current or potential public health importance. E.g. potential epidemic or multi-drug resistant health-care associated pathogen.
* Established bioinformatics pipelines (e.g. for AMR or serotyping) or extensions of current Pathogenwatch tools (e.g. core tree building, mlst, poppunk2).
* Community support for development and testing.
* Sufficient reference quality genome data for development and testing of genomics tools.

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If a genome is not identified by Speciator as belonging to a supported species, no further analyses will be undertaken. FASTA files and assembly QC statistics will be made available for download for a limited time before deletion of the genome and records.
{% endhint %}