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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.
Afiliación
  • Lancaster AK; Amber Biology LLC, Cambridge, MA, United States.
  • Single RM; Ronin Institute, Montclair, NJ, United States.
  • Mack SJ; Institute for Globally Distributed Open Research and Education (IGDORE), Cambridge, MA, United States.
  • Sochat V; Department of Mathematics and Statistics, University of Vermont, Burlington, VT, United States.
  • Mariani MP; Department of Pediatrics, University of California, San Francisco, Oakland, CA, United States.
  • Webster GD; Livermore Computing, Lawrence Livermore National Laboratory, Livermore, CA, United States.
Front Immunol ; 15: 1378512, 2024.
Article en En | MEDLINE | ID: mdl-38629078
ABSTRACT
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. Code available at https//zenodo.org/records/10080668 and https//github.com/alexlancaster/pypop.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Metagenómica Idioma: En Revista: Front Immunol Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Suiza
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Metagenómica Idioma: En Revista: Front Immunol Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Suiza