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

By John Lees, Marco Galardini, Stephen D. Bentley, Jeffrey N. Weiser, Jukka Corander

Posted 15 Feb 2018
bioRxiv DOI: 10.1101/266312 (published DOI: 10.1093/bioinformatics/bty539)

Summary: Genome-wide association studies (GWAS) in microbes face different challenges to eukaryotes and 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.

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