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

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 use...

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Autores principales: Lees, John A, Galardini, Marco, Bentley, Stephen D, Weiser, Jeffrey N, Corander, Jukka
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6289128/
https://www.ncbi.nlm.nih.gov/pubmed/30535304
http://dx.doi.org/10.1093/bioinformatics/bty539
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author Lees, John A
Galardini, Marco
Bentley, Stephen D
Weiser, Jeffrey N
Corander, Jukka
author_facet Lees, John A
Galardini, Marco
Bentley, Stephen D
Weiser, Jeffrey N
Corander, Jukka
author_sort Lees, John A
collection PubMed
description 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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spelling pubmed-62891282018-12-14 pyseer: a comprehensive tool for microbial pangenome-wide association studies Lees, John A Galardini, Marco Bentley, Stephen D Weiser, Jeffrey N Corander, Jukka Bioinformatics Applications Notes 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. Oxford University Press 2018-12-15 2018-07-02 /pmc/articles/PMC6289128/ /pubmed/30535304 http://dx.doi.org/10.1093/bioinformatics/bty539 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Lees, John A
Galardini, Marco
Bentley, Stephen D
Weiser, Jeffrey N
Corander, Jukka
pyseer: a comprehensive tool for microbial pangenome-wide association studies
title pyseer: a comprehensive tool for microbial pangenome-wide association studies
title_full pyseer: a comprehensive tool for microbial pangenome-wide association studies
title_fullStr pyseer: a comprehensive tool for microbial pangenome-wide association studies
title_full_unstemmed pyseer: a comprehensive tool for microbial pangenome-wide association studies
title_short pyseer: a comprehensive tool for microbial pangenome-wide association studies
title_sort pyseer: a comprehensive tool for microbial pangenome-wide association studies
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6289128/
https://www.ncbi.nlm.nih.gov/pubmed/30535304
http://dx.doi.org/10.1093/bioinformatics/bty539
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AT weiserjeffreyn pyseeracomprehensivetoolformicrobialpangenomewideassociationstudies
AT coranderjukka pyseeracomprehensivetoolformicrobialpangenomewideassociationstudies

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