<scp>EggLib</scp> 3: A <scp>python</scp> package for population genetics and genomics
Mathieu Siol, Thomas Coudoux, Sébastien Ravel, Stéphane De Mita
Abstract
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/.