RT Journal Article
SR Electronic
T1 Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 316976
DO 10.1101/316976
A1 Maxime Garcia
A1 Szilveszter Juhos
A1 Malin Larsson
A1 Pall I. Olason
A1 Marcel Martin
A1 Jesper Eisfeldt
A1 Sebastian DiLorenzo
A1 Johanna Sandgren
A1 Teresita Diaz de Ståhl
A1 Valtteri Wirta
A1 Monica Nistér
A1 Björn Nystedt
A1 Max Käller
YR 2018
UL http://biorxiv.org/content/early/2018/05/09/316976.abstract
AB Summary Whole-genome sequencing (WGS) is a cornerstone of precision medicine, but portable and reproducible open-source workflows for WGS analyses of germline and somatic variants are lacking. We present Sarek, a modular, comprehensive, and easy-to-install workflow, combining a range of software for the identification and annotation of single-nucleotide variants (SNVs), insertion and deletion variants (indels), structural variants, tumor sample heterogeneity, and karyotyping from germline or paired tumor/normal samples. Sarek is implemented in a bioinformatics workflow language (Nextflow) with Docker and Singularity compatible containers, ensuring easy deployment and full reproducibility at any Linux based compute cluster or cloud computing environment. Sarek supports the human reference genomes GRCh37 and GRCh38, and can readily be used both as a core production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups.Availability Source code and instructions for local installation are available at GitHub (https://github.com/SciLifeLab/Sarek) under the MIT open-source license, and we invite the research community to contribute additional functionality as a collaborative open-source development project.