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 (conda): https://anaconda.org/bioconda/pyseer
Download (pip): https://pypi.org/project/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.
Download (conda): https://anaconda.org/bioconda/poppunk
Download (pip): https://pypi.org/project/poppunk/
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.
Download (conda): https://anaconda.org/bioconda/seer
Download (github): https://github.com/johnlees/seer/releases