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PATO: Pangenome Analysis Toolkit

Miguel D. Fernández-de-Bobadilla, Alba Talavera-Rodríguez, Lucía Chacón, Fernando Baquero, Teresa M. Coque, Val F. Lanza
doi: https://doi.org/10.1101/2021.01.30.428878
Miguel D. Fernández-de-Bobadilla
1Department of Microbiology, University Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
3Bioinformatics Unit, University Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
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Alba Talavera-Rodríguez
2Department of Infectious Diseases, University Hospital Ramon y Cajal, IRYCIS, Madrid, Spain
3Bioinformatics Unit, University Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
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Lucía Chacón
3Bioinformatics Unit, University Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
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Fernando Baquero
1Department of Microbiology, University Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
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Teresa M. Coque
1Department of Microbiology, University Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
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Val F. Lanza
1Department of Microbiology, University Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
3Bioinformatics Unit, University Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
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  • For correspondence: valfernandez.vf@gmail.com
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Abstract

Motivation Comparative genomics is a growing field but one that will be eventually overtaken by sample size studies and the increase of available genomes in public databases. We present the Pangenome Analysis Toolkit (PATO) designed to simultaneously analyze thousands of genomes using a desktop computer. The tool performs common tasks of pangenome analysis such as core-genome definition and accessory genome properties and includes new features that help characterize population structure, annotate pathogenic features and create gene sharedness networks. PATO has been developed in R to integrate with the large set of tools available for genetic, phylogenetic and statistical analysis in this environment.

Results PATO can perform the most demanding bioinformatic analyses in minutes with an accuracy comparable to state-of-the-art software but 20–30x times faster. PATO also integrates all the necessary functions for the complete analysis of the most common objectives in microbiology studies. Lastly, PATO includes the necessary tools for visualizing the results and can be integrated with other analytical packages available in R.

Availability The source code for PATO is freely available at https://github.com/irycisBioinfo/PATO under the GPLv3 license.

Contact val.fernandez{at}salud.madrid.org

Supplementary information Supplementary data are available at Bioinformatics online

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/irycisBioinfo/PATO

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-NC-ND 4.0 International license.
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Posted February 01, 2021.
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PATO: Pangenome Analysis Toolkit
Miguel D. Fernández-de-Bobadilla, Alba Talavera-Rodríguez, Lucía Chacón, Fernando Baquero, Teresa M. Coque, Val F. Lanza
bioRxiv 2021.01.30.428878; doi: https://doi.org/10.1101/2021.01.30.428878
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PATO: Pangenome Analysis Toolkit
Miguel D. Fernández-de-Bobadilla, Alba Talavera-Rodríguez, Lucía Chacón, Fernando Baquero, Teresa M. Coque, Val F. Lanza
bioRxiv 2021.01.30.428878; doi: https://doi.org/10.1101/2021.01.30.428878

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