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Pathogenwatch focus species
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 are provided for each one.
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.
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.
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