Given a vector of sequences representing DNA fragments digested by two restriction enzymes (RE1 and RE2), the function will return fragments flanked by either the same restriction size (E1-E1 fragments typically for RESTseq method) or different restriction sites (RE1 and RE2, for ezRAD and ddRAD methods).
The function randomly generated DNA sequence of a given length and with fixed GC content to simulate DNA sequence representing a (proportion of the) genome for non-model species without available reference genome sequence.
Given a vector of sequences representing DNA fragments digested by restriction enzyme, the function return the DNA fragments that do not contain a specified restriction site, which is typically used to reduce the number of loci in the RESTseq method. The function can be use repeatedly for excluding fragments containing several restriction sites.
This function read a Fasta file containing a genome reference DNA sequence in the form of several contigs (or alternatively a single sequence) and can optionally randomly sub-select a fraction of the contigs sequence to allow for faster computation and avoid memory saturation.
SimRAD-package
(Package: SimRAD) :
Simulations to predict the number of loci expected in RAD and GBS approaches.
SimRAD provides a number of functions to simulate restriction enzyme digestion, library construction and fragments size selection to predict the number of loci expected from most of the Restriction site Associated DNA (RAD) and Genotyping By Sequencing (GBS) approaches. SimRAD aims to provide an estimation of the number of loci expected from a given genome depending on protocol type and parameters allowing to assess feasibility, multiplexing capacity and the amount of sequencing required.
Given a vector of sequences representing DNA fragments digested by one or several restriction enzymes, the function will return fragments within a specified size range which will simulate the size selection step typical of ddRAD, RESTseq and ezRAD methods.
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