Ipyrad: Interactive assembly and analysis of RADseq datasets

Abstract

ipyrad is a free and open source tool for assembling and analyzing restriction site-Associated DNA sequence datasets using de novo and/or reference-based approaches. It is designed to be massively scalable to hundreds of taxa and thousands of samples, and can be efficiently parallelized on high performance computing clusters. It is available both as a command line interface and as a Python package with an application programming interface, the latter of which can be used interactively to write complex, reproducible scripts and implement a suite of downstream analysis tools.