SimRAD: an R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches.
2014
Lepais, Olivier | Weir, Jason T | Ecologie Comportementale et Biologie des Populations de Poissons (ECOBIOP) ; Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA) | University of Toronto | European Union - OL was supported by a Marie Curie Action Career Integration Grant of the European Union FP7-PEOPLE-2011- CIG grant agreement number 303526. JW was supported by an NSERC Discovery Grant
International audience
Afficher plus [+] Moins [-]anglais. Application of high throughput sequencing platforms in the field of ecology and evolutionary biology is developing quickly since 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 develop SimRAD, an R package that performs in silico restriction enzyme digests and fragment size selection as implemented in most restriction 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. SimRAD 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. SimRAD is also useful for fine-tuning a given protocol to adjust the number of targeted loci. Here, we outline the functionality of SimRAD and provide an illustrative example of the use of the package (available on the CRAN at http://cran.r-project.org/web/packages/SimRAD)
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