RADinitio
Angel Rivera-Colón
Hello everyone,
We are happy to release RADinitio, a pipeline for the simulation of RADseq datasets. We originally began this work as part of the development of Stacks 2.0, as we had the need to generate datasets with known variants and library properties. We quickly realized that this sort of tool could be of benefit for users of Stacks and similar software to optimize the design of their RADseq experiments.
Using RADinitio, users can run several analyses including generating a RAD library from a population of simulated individuals, testing the number of extracted markers on a reference genome using different library configurations (we support both single and double-digest RAD libraries), testing the impacts of PCR amplification on duplicate reads, among others.
The first release of RADinitio is available on the Catchen Lab website, as well as instructions for installation and use. At the moment, we are working on an official publication for the software that should be out soon.
We are excited for members of the community to start using the software and strongly encourage your feedback. We hope it is of use when designing future RADseq experiments.
Thanks,
Angel
--
Angel G. Rivera-Colón
PhD Student, Catchen Lab
NSF IGERT VInTG Fellow
Department of Animal Biology
University of Illinois, Urbana-Champaign
@arcolon14