sv-gen

Highly portable parallel workflow to generate artificial genome data with structural variants.

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contributors
182 commits | Last update: March 24, 2020

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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.

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

Participating organizations

Contributors

  • 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

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