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SimRAD (version 0.96)

Simulations to Predict the Number of RAD and GBS Loci

Description

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 estimates the number of loci expected from a particular genome depending on the protocol type and parameters allowing to assess feasibility, multiplexing capacity and the amount of sequencing required.

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Version

Install

install.packages('SimRAD')

Monthly Downloads

39

Version

0.96

License

GPL-2

Maintainer

Olivier Lepais

Last Published

January 6th, 2016

Functions in SimRAD (0.96)

SimRAD-package

Simulations to predict the number of loci expected in RAD and GBS approaches.
insilico.digest.internal

Internal function to digest DNA sequence using one restriction enzyme.
ref.DNAseq

Function to import a reference DNA sequence from a Fasta file.
exclude.seqsite

Function to exclude fragments containing a specified restriction site.
size.select

Function to select fragments according to their size.
sim.DNAseq

Function to simulate randomly generated DNA sequence.
adapt.select

Function to select fragments according to the flanking restriction sites.
insilico.digest

Function to digest DNA sequence using one or two restriction enzyme(s).