sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data

PeerJ

article

Arnold Kuzniar¹  Jason Maassen¹  Stefan Verhoeven¹  Luca Santuari²  Carl Shneider²  Wigard P. Kloosterman²  Jeroen de Ridder² 

[1] Netherlands eScience Center;Center for Molecular Medicine, University Medical Center Utrecht

关键词: Scientific workflow;    Cancer genomics;    Variant calling;    Structural variants;    High-performance computing;    Cloud computing;    Snakemake;    Xenon;    Research software;    Open science;   

DOI  :  10.7717/peerj.8214

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases including cancer. Despite the advances in whole genome sequencing, comprehensive and accurate detection of SVs in short-read data still poses some practical and computational challenges. We present sv-callers, a highly portable workflow that enables parallel execution of multiple SV detection tools, as well as provide users with example analyses of detected SV callsets in a Jupyter Notebook. This workflow supports easy deployment of software dependencies, configuration and addition of new analysis tools. Moreover, porting it to different computing systems requires minimal effort. Finally, we demonstrate the utility of the workflow by performing both somatic and germline SV analyses on different high-performance computing systems.

【 授权许可】

CC BY