sv-gen

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

5
contributors

Cite this software

DOI:

10.5281/zenodo.3725663

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.

Keywords
  • Big data
  • High performance computing
  • Workflow technologies
Programming language
  • Python 96%
  • Shell 4%
License
  • Apache-2.0
</>Source code

Participating organisations

Netherlands eScience Center
University Medical Center Utrecht

Contributors

Contact person

Arnold Kuzniar

Arnold Kuzniar

Netherlands eScience Center
Mail Arnold
Arnold Kuzniar
Arnold Kuzniar
Netherlands eScience Center
Jason Maassen
Jason Maassen
Netherlands eScience Center
Lourens Veen
Lourens Veen
Netherlands eScience Center
LS
Luca Santuari
University Medical Center Utrecht
Stefan Verhoeven
Stefan Verhoeven
Netherlands eScience Center

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