/ebi-ngs-workshop

HGI's materials for the EBI Next Generation Sequencing (NGS) workshop

Primary LanguageTeX

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!