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The Popgen Pipeline Platform: A Software Platform for Facilitating Population Genomic Analyses

Andrew Webb, Jared Knoblauch, Nitesh Sabankar, Apeksha Sukesh Kallur, Jody Hey, Arun Sethuraman
doi: https://doi.org/10.1101/785774
Andrew Webb
1Center for Comptutational Genetics and Genomics, Temple University
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  • For correspondence: tug41380@temple.edu
Jared Knoblauch
1Center for Comptutational Genetics and Genomics, Temple University
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Nitesh Sabankar
2Department of Biological Sciences, California State University San Marcos
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Apeksha Sukesh Kallur
2Department of Biological Sciences, California State University San Marcos
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Jody Hey
1Center for Comptutational Genetics and Genomics, Temple University
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Arun Sethuraman
1Center for Comptutational Genetics and Genomics, Temple University
2Department of Biological Sciences, California State University San Marcos
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Abstract

Here we present the Pop-Gen Pipeline Platform (PPP), a software platform with the goal of reducing the computational expertise required for conducting population genomic analyses. The PPP was designed as a collection of scripts that facilitate common population genomic workflows in a consistent and standardized Python environment. Functions were developed to encompass entire workflows, including: input preparation, file format conversion, various population genomic analyses, output generation, and visualization. By facilitating entire workflows, the PPP offers several benefits to prospective end users - it reduces the need of redundant in-house software and scripts that would require development time and may be error-prone, or incorrect. The platform has also been developed with reproducibility and extensibility of analyses in mind. The PPP is an open-source package that is available for download and use at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html

Footnotes

  • ↵† jaredknoblauch{at}gmail.com

  • ↵‡ nsabankar{at}csusm.edu

  • ↵§ asukeshkall{at}csusm.edu

  • ↵¶ hey{at}temple.edu

  • ↵ǁ asethuraman{at}csusm.edu

  • https://ppp.readthedocs.io/en/latest/PPP_pages/install.html

  • https://www.csusm.edu/ppp/

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 September 30, 2019.
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The Popgen Pipeline Platform: A Software Platform for Facilitating Population Genomic Analyses
Andrew Webb, Jared Knoblauch, Nitesh Sabankar, Apeksha Sukesh Kallur, Jody Hey, Arun Sethuraman
bioRxiv 785774; doi: https://doi.org/10.1101/785774
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The Popgen Pipeline Platform: A Software Platform for Facilitating Population Genomic Analyses
Andrew Webb, Jared Knoblauch, Nitesh Sabankar, Apeksha Sukesh Kallur, Jody Hey, Arun Sethuraman
bioRxiv 785774; doi: https://doi.org/10.1101/785774

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