Comprehensive pangenome-wide association studies in microbes. Find genetic variation that is linked to a phenotype or clone of interest.
In collaboration with Marco Galardini.
Download (pip): https://pypi.org/project/pyseer
Download (conda): https://anaconda.org/bioconda/pyseer
Tools for bacterial genomic epidemiology. Quickly find core and accessory distances between whole-genome sequences, and use these to find genetically clusters. New data can be rapidly ‘queried’ against existing clusters, giving consistent nomenclature.
In collaboration with Nicholas Croucher.
First version of software for association studies in bacteria. Find k-mers that are linked to a phenotype of interest.
In collaboration with Jukka Corander.