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

View ORCID ProfileJohn A Lees, View ORCID ProfileMarco Galardini, View ORCID ProfileStephen D Bentley, Jeffrey N Weiser, View ORCID ProfileJukka Corander
doi: https://doi.org/10.1101/266312
John A Lees
1Department of Microbiology, New York University School of Medicine, New York, NY, 10016 USA,
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Marco Galardini
2European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, United Kingdom,
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Stephen D Bentley
3Infection Genomics, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom,
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Jeffrey N Weiser
1Department of Microbiology, New York University School of Medicine, New York, NY, 10016 USA,
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Jukka Corander
3Infection Genomics, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom,
4Department of Biostatistics, University of Oslo, 0372 Oslo, Norway
5Helsinki Institute of Information Technology (HIIT), Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
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Abstract

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.

Contact john.lees{at}nyumc.org and marco{at}ebi.ac.uk

Supplementary information Supplementary data are available online.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 15, 2018.
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pyseer: a comprehensive tool for microbial pangenome-wide association studies
John A Lees, Marco Galardini, Stephen D Bentley, Jeffrey N Weiser, Jukka Corander
bioRxiv 266312; doi: https://doi.org/10.1101/266312
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pyseer: a comprehensive tool for microbial pangenome-wide association studies
John A Lees, Marco Galardini, Stephen D Bentley, Jeffrey N Weiser, Jukka Corander
bioRxiv 266312; doi: https://doi.org/10.1101/266312

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