EggLib 3: A python package for population genetics and genomics

Siol Mathieu, Coudoux Thomas, Ravel Sébastien, De Mita Stéphane. 2022. EggLib 3: A python package for population genetics and genomics. Molecular Ecology Resources, 22 (8) : 3176-3187.

https://doi.org/10.1111/1755-0998.13672

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Résumé : Rapid and repeatable polymorphism analyses have become a necessity with the current amount of genomic data that can be collected in many organisms. Traditionally, such analyses are conducted using a variety of tools in combination, often requiring numerous format translation and manipulation. Here, we present a massively updated version of our previous software package egglib, intended to alleviate such costly and error-prone tinkering with the data. egglib has been streamlined into a python package and thoroughly updated and optimized to accommodate modern-day sized dataset. We show the main characteristics of the package making it a tool of choice to perform population genetics analyses. Once the data are imported (whatever their encoding), they can be filtered, edited, analysed and compared to coalescent simulations very easily and efficiently. Furthermore, the list of diversity and polymorphism statistics that can now be calculated has been greatly expanded. The software and its full documentation are available at https://egglib.org/.

Mots-clés Agrovoc : polymorphisme génétique, génétique des populations, génome, collecte de données, génomique, variété, conditionnement

Mots-clés libres : Coalescent simulations, Diversity statistics, Polymorphism, Population genomics, PYTHON

Agences de financement hors UE : Agence Nationale de la Recherche

Projets sur financement : (FRA) Génomique et adaptation des traits de vie des champignons impliqués dans les interactions plante-pathogène

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