Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants.
Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants.
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DOI：
10.12688/f1000research.16665.2
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发表时间：
2020-01-01
期刊：
影响因子：
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通讯作者：
Nystedt, Bjorn
中科院分区：
文献类型：
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作者：
Garcia, Maxime;Juhos, Szilveszter;Nystedt, Bjorn
全基因组测序（WGS）是推进精准医学研究的基础技术，但用于WGS分析的便携式和用户友好的工作流程有限，这对许多研究小组构成了重大挑战，并阻碍了科学进步。在这里，我们介绍了Sarek，一个开源的工作流程，用于基于来自WGS，全外显子组测序（WES）或基因组的测序数据检测种系变异和体细胞突变。Sarek的特点是（i）易于安装，（ii）在不同的计算机环境中具有强大的可移植性，（iii）全面的文档，（iv）透明且易于阅读的代码，以及（v）广泛的质量指标报告。Sarek是用Nextflow工作流语言实现的，支持Docker和Singularity容器以及Conda环境，使其成为在任何POSIX兼容计算机和云计算环境上轻松部署的理想选择。Sarek遵循GATK关于读段比对和预处理的最佳实践建议，并包括用于识别和注释生殖系和体细胞单核苷酸变异、插入和缺失变异、结构变异、肿瘤样本纯度以及倍性和拷贝数变异的广泛软件。Sarek提供简单、高效和可重复的WGS分析，可以很容易地用作测序设施的生产工作流程，也可以用作单个研究小组的强大独立工具。Sarek源代码、文档和安装说明可在https://github.com/nf-core/sarek和https://nf-co.re/sarek/上免费获得。
Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at https://github.com/nf-core/sarek and at https://nf-co.re/sarek/.