Core Genome Tree
About
For a curated set of species Pathogenwatch provides the ability to construct a tree based on a core genome distance, along with assignment to a closest reference genome in a taxonomically representative set. The core genome and parameters are tested for each in species in turn, using a combination of manual validation against published datasets and automated validation against "gold standard" trees.
Methods
The approach can be split into four separate stages, described in their own sections:
How to cite
The core genome tree process is first described in Harris SR, Cole MJ, Spiteri G, et al. Public health surveillance of multidrug-resistant clones of Neisseria gonorrhoeae in Europe: a genomic survey. Lancet Infect Dis. 2018;18(7):758-768. doi:10.1016/S1473-3099(18)30225-1
The software are is available under an OSS licence from https://github.com/pathogenwatch-oss/core-fp and https://github.com/pathogenwatch-oss/tasks.
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