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- Title
Sim RAD: an R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches.
- Authors
Lepais, Olivier; Weir, Jason T.
- Abstract
Application of high-throughput sequencing platforms in the field of ecology and evolutionary biology is developing quickly with the introduction of efficient methods to reduce genome complexity. Numerous approaches for genome complexity reduction have been developed using different combinations of restriction enzymes, library construction strategies and fragment size selection. As a result, the choice of which techniques to use may become cumbersome, because it is difficult to anticipate the number of loci resulting from each method. We developed Sim RAD, an R package that performs in silico restriction enzyme digests and fragment size selection as implemented in most restriction site associated DNA polymorphism and genotyping by sequencing methods. In silico digestion is performed on a reference genome or on a randomly generated DNA sequence when no reference genome sequence is available. Sim RAD accurately predicts the number of loci under alternative protocols when a reference genome sequence is available for the targeted species (or a close relative) but may be unreliable when no reference genome is available. Sim RAD is also useful for fine-tuning a given protocol to adjust the number of targeted loci. Here, we outline the functionality of Sim RAD and provide an illustrative example of the use of the package (available on the CRAN at ).
- Subjects
YACHTING; MARINE electronics; FISHERIES; BIOLOGICAL evolution; MARINE ecology
- Publication
Molecular Ecology Resources, 2014, Vol 14, Issue 6, p1314
- ISSN
1755-098X
- Publication type
Article
- DOI
10.1111/1755-0998.12273