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. 2018 Dec 15;34(24):4310-4312.
doi: 10.1093/bioinformatics/bty539.

pyseer: a comprehensive tool for microbial pangenome-wide association studies

John A Lees  1 , Marco Galardini  2 , Stephen D Bentley  3 , Jeffrey N Weiser  1 , Jukka Corander  3   4   5
Affiliations

pyseer: a comprehensive tool for microbial pangenome-wide association studies

John A Lees et al. Bioinformatics. .

Abstract

Summary: Genome-wide association studies (GWAS) in microbes have different challenges to GWAS in eukaryotes. These have been addressed by a number of different methods. pyseer brings these techniques together in one package tailored to microbial GWAS, allows greater flexibility of the input data used, and adds new methods to interpret the association results.

Availability and implementation: pyseer is written in python and is freely available at https://github.com/mgalardini/pyseer, or can be installed through pip. Documentation and a tutorial are available at http://pyseer.readthedocs.io.

Supplementary information: Supplementary data are available at Bioinformatics online.

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