This lesson is still being designed and assembled (Pre-Alpha version)

Genotype by Sequencing: Setup


This workshop is designed to be conducted on the NeSI compute infrastructure. All software and data is already set up for you to use during the workshop.

Running the workshop locally on your own computer will involve installing the required programs and downloading the example data. Some software packages may not work on all operating systems. Below are the requirements for running locally.


The software needed to run this lesson are listed below. Versions reported are the ones we use on NeSI but the lesson is likely to work with a range of versions of these softwares.

Software Version Manual Description
Stacks 2.58 link GBS/RAD-Seq SNP calling pipeline.
BWA 0.7.17 link Mapping DNA sequences.
SAMtools 1.9 link Utilities for manipulating alignments in the SAM format.
R 4.1.0 link Statistical computing language.

The following R packages are alse required:


The files associated with this lesson can be downloaded separately here.

The data used in this workshop comes from:

Ingram, T., Dutoit, L., Mikheev, P., Khan, S., & Schallenberg, M. (2020). Phenotypic, ecological, and genomic variation in common bully (Gobiomorphus cotidianus) populations along depth gradients in New Zealand’s southern Great Lakes. Canadian Journal of Fisheries and Aquatic Sciences, 77(10), 1678-1687. doi:0.1139/cjfas-2020-0015

The files mentioned can be downloaded here.