Highly portable parallel workflow to generate artificial genomes with structural variants.

183 commits | Last update: June 29, 2020

Cite this software

Choose a version:
[[ releases.length > 0 ? releases[selectedIndex].doi : conceptDOI ]]
Copy to clipboard
Choose a reference manager file format:
Download file

What sv-gen can do for you

  • 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.

Read more
  • High performance computing
  • Workflow technologies
  • Big data
Programming Language
  • Python
  • Java
  • Apache-2.0
Source code

Participating organizations


  • Arnold Kuzniar
    Netherlands eScience Center
  • Luca Santuari
    University Medical Center Utrecht
  • Lourens Veen
    Netherlands eScience Center
  • Stefan Verhoeven
    Netherlands eScience Center
  • Jason Maassen
    Netherlands eScience Center
Contact person
Arnold Kuzniar
Netherlands eScience Center

Information for page maintainers

OAI-PMH metadata:
citation metadata: