EBI Next Generation Sequencing (NGS) Workshop

Download

Clone the repository and then checkout the large files with Git LFS:

git clone git@github.com:wtsi-hgi/ebi-ngs-workshop.git
cd ebi-ngs-workshop
git lfs checkout

Note: Some git versions/setups download the large files during the clone.

Build

To build the course materials, run build.sh (requires docker).

Deployment

Software Requirements

• eog
• IGV
• bcftools 1.7+
• samtools 1.7+
• gnuplot
• An image viewer capable of opening PDFs, configured with xdg-open
• matplotlib Python module
• picard-tools
• vcftools (ensure vcf-annotate works)
• LaTeX
• vim and emacs

Materials

• Ideally, bake the material into the student's home directory on the VM image.
• Provide a read-only backup tar on the remote drive, which will allow students who accidentally destroy files to recover!