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sv-gen

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

5
contributors

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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
Programming languages
  • Python 96%
  • Shell 4%
License
</>Source code

Participating organisations

Netherlands eScience Center
University Medical Center Utrecht

Contributors

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