Software

pyseer

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
Paper:  https://doi.org/10.1093/bioinformatics/bty539
Documentation: https://pyseer.readthedocs.io
Code: https://github.com/mgalardini/pyseer

PopPUNK

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 (pip): https://pypi.org/project/poppunk/
Paper: https://doi.org/10.1101/360917
Documentation: https://poppunk.readthedocs.io
Code: https://github.com/johnlees/poppunk

SEER

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: https://github.com/johnlees/seer/releases
Paper: https://doi.org/10.1038/ncomms12797
Documentation: https://github.com/johnlees/seer/wiki
Code: https://github.com/johnlees/seer