# cgMLST

## About

cgMLST schemes are based around a community-agreed set of gene loci present in all strains of the species. A database of validated allele sequences is maintained for each locus and a code assigned to each one. An "ST" code is then generated from the unique combination alleles. The schemes supported by Pathogenwatch are provided by [PubMLST](https://pubmlst.org/), the [Pasteur Institute](http://bigsdb.pasteur.fr/), [Enterobase](https://enterobase.warwick.ac.uk/), and the [cgMLST.org Nomenclature Server,](https://www.cgmlst.org/ncs) while an in-house search tool is used to rapidly but accurately assign the correct cgMLST assignment.

{% hint style="info" %}
If your profile includes novel alleles or a novel MLST code, we recommend visiting the source database linked in the results page to submit your genome there. Generated assignments will be subsequently be imported in Pathogenwatch at the next update.
{% endhint %}

## Method

The assembly is searched for exact matches to known alleles. A representative set of alleles for each locus are then searched for using BLAST. These searches are combined and filtered based on the similarity of the match and length of the match. Novel alleles are hashed using the SHA-1 algorithm, this is then used as their unique identifier. Profiles are assigned based on the combination of alleles detected. Novel profiles are also given a unique identifier using the [SHA-1 hash algorithm](https://en.wikipedia.org/wiki/SHA-1).

## Results

The cgMLST results are not displayed directly, but are available as a download from both collection and genome selection download menus. The results also serve as the basis for the [cgMLST clustering method](/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/cgmlst-clustering.md) for quickly finding closely related assemblies.

## How to cite

Please cite the resource which hosts the cgMLST scheme. The host of the scheme should linked in individual genome reports. Please contact us if you have any questions.

The software is available under an OSS licence from <https://github.com/pathogenwatch-oss/mlst> and <https://github.com/pathogenwatch-oss/typing-databases>.


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