SoftwareApplication
identifier: 10.5281/zenodo.1217111
name: sv-callers
description: Highly portable parallel workflow to detect structural variants in cancer genomes.
description: * 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](https://snakemake.readthedocs.io/)-based workflow combines several state-of-the-art tools (i.e. [Manta](https://github.com/Illumina/manta), [DELLY](https://github.com/dellytools/delly), [LUMPY](https://github.com/arq5x/lumpy-sv) and [GRIDSS](https://github.com/PapenfussLab/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.
code repository: https://github.com/GooglingTheCancerGenome/sv-callers
author: Person
  given name: Luca
  family name: Santuari
  name: Luca Santuari
  affiliation: Organization
    name: University Medical Center Utrecht
author: https://orcid.org/0000-0002-8172-4865
author: https://orcid.org/0000-0003-1711-7961
author: https://orcid.org/0000-0002-5821-2060
keywords: Workflow technologies
keywords: High performance computing
keywords: Big data
programming language: Python
programming language: Shell
license:
  creative work: creativeWork
    name: Apache-2.0
reference publication: peerj.8214
reference publication: escience.2018.00064
reference publication: 2024.10.17.618894

https://orcid.org/0000-0002-8172-4865
type: Person
given name: Jason
family name: Maassen
name: Jason Maassen
affiliation: Organization
  name: Netherlands eScience Center

https://orcid.org/0000-0003-1711-7961
type: Person
given name: Arnold
family name: Kuzniar
name: Arnold Kuzniar

https://orcid.org/0000-0002-5821-2060
type: Person
given name: Stefan
family name: Verhoeven
name: Stefan Verhoeven
affiliation: Organization
  name: Netherlands eScience Center

peerj.8214
type: ScholarlyArticle
name: sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data
pagination: e8214
url: https://doi.org/10.7717%2Fpeerj.8214

escience.2018.00064
type: ScholarlyArticle
name: A portable and scalable workflow for detecting structural variants in whole-genome sequencing data
pagination: 303-304
url: https://doi.org/10.1109%2Fescience.2018.00064

2024.10.17.618894
type: ScholarlyArticle
name: sv-channels: filtering genomic deletions using one-dimensional convolutional neural networks
url: https://doi.org/10.1101%2F2024.10.17.618894