sv-gen

• Generates artificial short-read alignments including different types of structural variants (SVs)
• Enables scalable and portable genome simulations across HPC clusters (e.g., using GridEngine, Slurm etc.) or compute clouds
• It's easy to use, deploy and extend with new tools

This Snakemake-based workflow generates artificial short-read alignments based on a reference genome with(out) SVs. The workflow is easy to use and deploy on any Linux-based machine. In particular, the workflow supports automated software deployment, easy configuration and addition of new analysis tools as well as enables to scale from a single computer to different HPC clusters with minimal effort.