sv-callers

Highly portable parallel workflow to detect structural variants in cancer genomes.

10
mentions
4
contributors

Cite this software

DOI:

10.5281/zenodo.1217111

What sv-callers can do for you

  • Enables comprehensive detection of structural variants (SVs) by combining multiple tools
  • Supports both single-sample (germline) and paired-sample (somatic) SV analyses
  • Makes the analyses scalable and easily portable 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 combines several state-of-the-art tools (i.e. Manta, DELLY, LUMPY and GRIDSS) for detecting structural variants (SVs) in whole genome sequencing data. The workflow is easy to use and to 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 94%
  • Shell 6%
License
  • Apache-2.0
</>Source code

Participating organisations

Netherlands eScience Center
University Medical Center Utrecht

Mentions

Portable HPC workflows with Snakemake, Conda, and Xenon

Author(s): Jurriaan H. Spaaks
Published in 2018

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
LS
Luca Santuari
University Medical Center Utrecht
Stefan Verhoeven
Stefan Verhoeven
Netherlands eScience Center

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