Restriction site-associated DNA from Python-implemented Digestion Simulations (RApyDS): a companion tool for RAD sequencing experimental design

Abstract

Reduced representation sequencing is a practical approach for obtaining genetic variations from a random subsample of the genome. RADseq (Restriction Site-Associated DNA Sequencing), as one of the more popular reduced representation approaches, is currently being used in a wide array of applications including marker development, phylogenetics, and population genomics. A crucial step in designing a RADseq experiment is the selection of one or a pair of restriction enzymes (RE) that will result in sufficient density of loci to meet the objectives of the study, which is not straightforward because of difficulties in obtaining a standard set of REs that can generally be applied to RADseq experimental designs. Here we present RApyDS, a simulation tool that provides users with evaluation metrics to aid in choosing suitable REs based on their target RADseq design. RApyDS can perform simulations for single- or double-digest RADseq, preferably with a supplied reference genome. The tool outputs an overview page, electrophoresis visualization, mapping of restriction cut sites, and RAD loci density across the genome. If supplied with an annotation file, the program can also output evaluation metrics for a specified genomic feature. The tool is currently available at https://github.com/pgcbioinfo/rapyds.