The Pop-Gen Pipeline Platform (PPP) is a software platform for 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, and output generation. 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
11Here we present the Pop-Gen Pipeline Platform (PPP), a software platform 12 with the goal of reducing the computational expertise required for conducting 13 population genomic analyses. The PPP was designed as a collection of scripts 14 that facilitate common population genomic workflows in a consistent and stan-15 dardized Python environment. Functions were developed to encompass entire 16 workflows, including: input preparation, file format conversion, various popu-17 lation genomic analyses, output generation, and visualization. By facilitating 18 entire workflows, the PPP offers several benefits to prospective end users -it 19 reduces the need of redundant in-house software and scripts that would re-20 quire development time and may be error-prone, or incorrect. The platform has 21 also been developed with reproducibility and extensibility of analyses in mind. 22 The PPP is an open-source package that is available for download and use at 23 https://ppp.readthedocs.io/en/latest/PPP_pages/install.html 24 Since the advent of genomics, population genetics has quickly become domi-26 nated by complex statistical and computational methodologies [1, 2]. An un-27 fortunate consequence of this fact is that many investigators lack the necessary 28 resources -computational, and time -to independently implement many of these 29 methodologies. This inevitably requires investigators to select from a plethora 30 of software (i.e. analytical tools) that have been developed by other researchers. 31While this is not inherently a problem, and a common practice among many 32 professions, it is not without its own difficulties. Investigators frequently face 33 bespoke input and output formats that may not be accompanied by an intuitive 34 and easy-to-use file-format conversion software, implementations that may be 35 complex and open to misinterpretation, and lastly implementations incapable 36 of large-scale analyses.These challenges are further amplified as few analyses re-37 quire a single tool, but rather require an analytical pipeline. Analytical pipelines 38 typically incorporate a number of methodologies and software designed specifi-39 cally to connect those methodologies in a specific order. 40The challenges posed by analytical pipelines have been partially mitigated by 41 the development of software packages or "tool-kits" that provide tools for a 42 variety of methodologies. However, while popular packages such as vcftools 43 [3], bcftools [4], and plink [5] have proven invaluable to many investigators, 44 they cannot be all-encompassing. The absence of such tool-kits often requires 45 investigators, if able, to create pipelines that are frequently recreated, infre-46 quently published, time consuming to develop, and susceptible to error. For 47In an attempt to greatly alleviate these obstacles we have developed the Pop- 51Gen Pipeline Platform (PPP). The PPP was designed to be a comprehensive 52 platform wherein investigators can conduct many of the analytical pipelines in-53 volved in population genomics in ...
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