PyPop: Python For Population Genomics


Amber Biology has been engaged to perform a full-scale overhaul of Python for Population Genomics (PyPop). PyPop is an open-source framework for large-scale population genomics. implemented to probe genotype data for signatures of natural selection.  It has been used extensively in the population and statistical genetics community, and has contributed to over 170 peer-reviewed scientific articles.

Amber Biology has worked on scaling-up of the Python and C codebase to enable PyPop to process up to 500,000 individual genotypes; to enable the application to parse a new allele nomenclature; to modernize the code by replacing deprecated code libraries with current ones, and to fix bugs and refactor the code to make it cleaner and easier to maintain.  PyPop is now being actively used to process data for the NIH-funded International HLA and Immunogenetics Workshop, and is integrated into the National Institute of Allergy and Infectious Diseases (NIAID’s) immunology data management portal ImmPort.

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ProjectAlex Lancaster