> 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/technical-descriptions-of-analysis-tools/lineage-and-genotyping/geno7pet.md).

# Geno7PET

## About

Since the 1960s, the 7PET pandemic lineage of *Vibrio cholerae* has split into many sublineages (e.g. AFR10, AFR15, BD2, etc.). Geno7PET is an *in silico* genotyping method for assigning 7PET genomes to 7PET sublineages, based on signature SNPs (single nucleotide polymorphisms) for each sublineage. This approach can assign genomes to known 7PET sublineages, e.g. 7PET sublineage AFR10 is classified to Geno7PET class 3.1.4 (see [github.com/avrilcoghlan/geno7PET](https://github.com/avrilcoghlan/geno7PET) for further details)."

In Pathogenwatch, the 7PET lineage corresponds to PopPUNK cluster "1", so the result is only displayed in the genome reports and collection view if the genome has been assigned to that cluster. Results are shown for non-7PET lineages in the CSV download, but these should be disregarded.

{% hint style="info" %}
For more information on interpreting Geno7PET results, please see the documentation provided by Vibriowatch: <https://vibriowatch.readthedocs.io/en/latest/mlst.html>
{% endhint %}

## How to cite

Please see the documentation at <http://github.com/avrilcoghlan/geno7PET/blob/main/README.md>