Mac set-up for RADseq

Here you will find a list of usefull programs and R packages usefull for performing RADseq studies.

BASH commands

Get Xcode

xcode-select --install

Install Homebrew

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Install GDAL

brew install gdal --HEAD

Install SHUFF command

brew install coreutils

Install wget

brew install wget

Install gsl

brew install gsl

PROGRAMS

Install FILEZILLA

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" < /dev/null 2> /dev/null ; brew install caskroom/cask/brew-cask 2> /dev/null
brew cask install filezilla

Install VCFTOOLS

VCFtools is a program package designed for working with VCF files, such as those generated by STACKS.

brew install vcftools

Install PLINK

PLINK is a free, open-source whole genome association analysis toolset, designed to perform with tfam and tped files that are easily converted from vcftools via the plink-tped following command:

vcftools --vcf nameofyourfile.vcf --plink-tped --out nameofyourfile
done

Install JAVA

brew cask install java
brew cask info java

Install PGDSpider

PGDSpider is a data conversion tool for population genetic and genomics programs. It support a vast range of data types with the ability of parsing 33 and writing 36 different file formats

Install ADMIXTURE

ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. To use ADMIXTURE, you need to transfor your file vcf file into a bed format via plink by typing the make-bed command available in PLINK:

plink --tfam nameofyourfile.tfam --tped nameofyourfile.tped --make-bed --out nameofyourfile
done

Install BEDOPS

git clone https://github.com/bedops/bedops.git
cd bedops
make
make install

Install R studio

R studio has developped an integrated development environment for R, with a console that supports direct code execution.

brew cask install xquartz
brew cask install r
brew cask install --appdir=/Applications rstudio

R software: install R packages

First install devtools package that allows you to directly download R package available in github.

install.packages("devtools")

Then, a variety of useful package for population genomics such as adegenet, strataG, assigner are available in R.

install.packages("adegenet")
install.packages("strataG")
install.packages("assigner")
install.packages("radiator")
install.packages("ape")
install.packages("poppr")
install.packages("hierfstat")
install.packages("dartR")
install.packages("StAMPP")
install.packages("genetics")
install.packages("LDna")
install.packages("ade4")
devtools::install_github('royfrancis/pophelper')
devtools::install_github("thierrygosselin/assigner")

Set up your bash profile in MacOs Catalina

First, create a folder named 00-Programs and placed it in your local environment, with a short cut access. In this folder you will enter all the binaies that you need to use for running programs such as admixture, Bayescan or VCFTOOLS for instance.

Create your bash_profile that is now named zprofile in macOS Catalina and update it with the sourcecommand.

nano ~/.zprofile
source ~/.bash_profile

Add this folder path to your zprofile file.

export PATH=$PATH:/Users/laurabenestan/Dropbox/02-Bio-informatics/00-Programs