Applications of Admixture Genomics (UE UniVienna).

This repo contains the materials for practical sessions, and will be updated accordingly.

To use these materials, you can click the badge , which will create an online virtual machine containing the tools and data used in the practical sessions.

Or you can download this repo and install the dependencies with miniconda in your local machine using the following commands. To install miniconda, you can follow the instruction here.

git clone https://github.com/admixVIE/appladmix
cd appladmix
conda env create -f environment.yml
conda activate appladmix

At the moment, there are the following modules:

• Basics in bash and handing of sequencing data ("1_basics").
• VCF files and bcftools; with Challenge ("2_data")
• Admixtools, f/D-statistics & intro to R ("3_admixtools")
• Introgression detection with sstar; with Challenge ("4_introgression")

In the near future, the first session (basics in bash) shall be optional (or in preparation), and it will be a requirement for the course to know how to bash.

Planned modules are:

• Explorative data analysis with PCA, clustering and NGStools
• Handling amd exploring ancient DNA sequencing data
• Introgression detection with gaia (in development)
• Simulating data