PyPop: a mature open-source software pipeline for population genomics

Lancaster, Alexander K.; Single, Richard M.; Mack, Steven J.; Sochat, Vanessa; Mariani, Michael P.; Webster, Gordon D.

doi:10.3389/fimmu.2024.1378512

Title: PyPop: a mature open-source software pipeline for population genomics

Journal Article · 02 April 2024 · Frontiers in Immunology

DOI: https://doi.org/10.3389/fimmu.2024.1378512 · OSTI ID:2471181

Lancaster, Alexander K. ^[1]; Single, Richard M. ^[2]; Mack, Steven J. ^[3]; Sochat, Vanessa ^[4]; Mariani, Michael P. ^[5]; Webster, Gordon D. ^[6]

Amber Biology LLC, Cambridge, MA (United States); Ronin Institute, Montclair, NJ (United States); Institute for Globally Distributed Open Research and Education (IGDORE), Cambridge, MA (United States)
Univ. of Vermont, Burlington, VT (United States)
Univ. of California, San Francisco, CA (United States)
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Univ. of Vermont, Burlington, VT (United States); Mariani Systems LLC, Hanover, NH (United States)
Amber Biology LLC, Cambridge, MA (United States); Ronin Institute, Montclair, NJ (United States)

Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well. Here, we present PyPop 1.0.0, a new major release of the package, which implements new features using the more robust infrastructure of GitHub, and is distributed via the industry-standard Python Package Index. New features include implementation of the asymmetric linkage disequilibrium measures and, of particular interest to the immunogenetics research communities, support for modern nomenclature, including colon-delimited allele names, and improvements to meta-analysis features for aggregating outputs for multiple populations.

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Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC52-07NA27344

OSTI ID:: 2471181

Journal Information:: Frontiers in Immunology, Journal Name: Frontiers in Immunology Vol. 15; ISSN 1664-3224

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
97 MATHEMATICS AND COMPUTING
HLA
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immunology
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Title: PyPop: a mature open-source software pipeline for population genomics

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