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:

1. Core Assignment

2. Reference Assignment

3. Filtering

4. Tree Construction

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.