Installation

Downloading ISSRseq Pipeline Scripts

To clone the most recent version of the ISSRseq pipeline, execute the following commands:

git clone https://github.com/btsinn/ISSRseq.git

cd ISSRseq

chmod +x *.sh

Then, ensure you can execute the ISSRseq scripts when in any directory by including the ISSRseq directory into your path variable. Execute the following, replacing the 'full_path_to_ISSRseq_dir' portion of the line below with the full path to your ISSRseq directory:

export PATH=$PATH:full_path_to_ISSRseq_dir]

Pipeline Dependencies:

The ISSRseq pipeline depends on multiple programs, which the user will need to properly install each and be sure to include them in their system path.

We do not supply an installation script or support for these programs, each of which is well documented by its own developer.

Tested on Ubuntu Linux 16.04 and 18.04 LTS -- no other OS tested.

abyss-PE (version 2.2.4)
samtools (1.7 -- apt-get install samtools)
picard tools (version 2.22.8)
GATK (version 4.1.8.0)
vcf2phylip (version 2)
vcftools (version 0.1.17)
pigz (2.4-1 -- apt-get install pigz)
BBMap and BBDUK (38.51)

BLAST Database configuration if using ISSRseq_AssembleReference.sh:

Prior to using ISSRseq_AssembleReference.sh, the user must create a BLAST database comprising genomes of organisms that they expect as contaminants (see instructions here).

Once the database is created, open the ISSRseq_AssembleReference script in a plain text editor and replace the path shown below with the path to the created BLAST database. The path is everything after the = sign:

BLASTDB=/usr/local/src/ISSRseq/contam_filters/default_contam_filter_BLASTDB/default_contam_filter.fasta

The following packages are required to conduct population genomic analyses using the supplied R script:

Package for data processing from VCF file

install.packages("vcfR")

Packages for population genetic analyses (AMOVA, bootstrapping ect.)

install.packages("poppr")
install.packages("adegenet")
install.packages("ape")
install.packages("mmod")
install.packages("magrittr")
install.packages("hierfstat")
install.packages("pegas")
install.packages("qvalue")

Package for local adaptation analysis

install.packages("pcadapt")

Package for admixture analysis

install.packages("LEA")

Packages for figures and plots

install.packages("ggplot2")
install.packages("plot3D")
install.packages("plotly")
install.packages("igraph")
install.packages("RColorBrewer")
install.packages("grid")
install.packages("R.devices")

Package for Wes Anderson themed color palettes (Range 4-5 colors). Choices are: BottleRocket1, BottleRocket2, Rushmore1, Royal1, Royal2, Zissou1, Darjeeling1, Darjeeling2, Chevalier1, FantasticFox1, Moonrise1, Moonrise2, Moonrise3, Cavalcanti1, GrandBudapest1, GrandBudapest2, IsleofDogs1, IsleofDogs2

install.packages("wesanderson")