Abstract
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/.
Highlights
Whole-genome sequencing (WGS) and whole-exome sequencing (WES) technologies opens up new avenues for research and for clinical applications, with many large initiatives launched worldwide
While much effort has been invested in novel sequencing analysis software, the importance of providing and maintaining workflows to combine software in an efficient and reproducible manner has been underestimated and too few resources are typically dedicated to address this issue. This is of particular importance for somatic variant analysis and especially for analysis of complex cancer genomes, where a combination of tools is still required for optimal sensitivity and specificity and to detect various types of gene mutations and other abnormalities (Alioto et al, 2015)
Operation: Workflow overview and software Sarek offers a portable workflow for germline and somatic variant detection, annotation and quality control based on WGS, WES or gene panel data, using a range of state-of-the-art software and data resources in the field (Table 1, Figure 1)
Summary
Whole-genome sequencing (WGS) and whole-exome sequencing (WES) technologies opens up new avenues for research and for clinical applications, with many large initiatives launched worldwide. While much effort has been invested in novel sequencing analysis software, the importance of providing and maintaining workflows to combine software in an efficient and reproducible manner has been underestimated and too few resources are typically dedicated to address this issue. This is of particular importance for somatic variant analysis and especially for analysis of complex cancer genomes, where a combination of tools is still required for optimal sensitivity and specificity and to detect various types of gene mutations and other abnormalities (Alioto et al, 2015). By using Docker or Singularity containers, Sarek installs on all POSIX compatible systems such as Linux and Mac OS X and is designed to work on compute environments dedicated to handle sensitive personal data without direct internet access—a situation expected to become increasingly common with growing data security awareness
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