Population Genomics

Structure

module spider Structure

The program structure is a free software package for using multi-locus genotype data to investigate population structure.

After loading the Structure module, copy the two params files to your working directory and edit as needed:

module load GCC/8.3.0 Structure/2.3.4
cp $EBROOTSTRUCTURE/bin/*params ./

StrAuto

GCATemplates available: no

StrAuto manual

Automation and Parallelization of STRUCTURE Analysis

StrAuto is the first tool to integrate STRUCTURE analysis with post-processing using a pipeline approach in addition to implementing parallel computation – a set up ideal for deployment on computing clusters.

After loading the StrAuto module, copy the two Structure params files to your working directory and edit each as needed:

cp $EBROOTSTRUCTURE/bin/*params ./

Stacks

GCATemplates * Ada (ustacks)

Stacks homepage

module spider Stacks

Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

When running Stacks , be sure to specify the number of threads by adding the following UNIX environment variable to your job script

export OMP_NUM_THREADS=20

ipyrad

GCATemplates available: no

ipyrad is a toolbox for assembly and analysis of RAD-seq type genomic data sets. Notably, it has four assembly methods by which to assemble data: denovo, reference, reference addition, and reference subtraction.

ipyrad can be installed as a shared Anaconda environment per request.