RADinitio
Description
RADinitio is a pipeline for the assessment of RADseq experiments via prospective and retrospective data simulation. Sequencing data is generated de novo from a population of individuals via a coalescent simulation under a user-defined demographic model using msprime. The genetic variants in each sample are simulated in a genomic context that can i mpact downstream generation of RAD loci and sequencing reads. The per-individual sequences are then treated to an in silico RADseq library preparation. The components of the library are defined by the user, allowing for the exploration of parameters including restriction enzyme selection, insert size, sequencing coverage, and PCR duplicate distribution (generated using the decoratio software). RADinitio simulations can also be applied retrospectively by comparing and modelling sources of error in empirical datasets. The purpose of RADinitio is for researchers to fully explore possible variables in their data generation process to ensure that their protocol selection and library preparation is performed optimally, within the limitations of technical and experimental error.
Environment Modules
Run module spider radinitio to find out what environment modules are available for this application.
System Variables
- HPC_RADINITIO_DIR - installation directory
- HPC_RADINITIO_BIN - executable directory
Citation
If you publish research that uses radinitio you have to cite it as follows:
Rivera-Colón AG, Rochette NC, Catchen JM. (2021) Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data. Mol Ecol Resour 21: 363-378. DOI: 10.1111/1755-0998.13163