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Treffer: Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

Title:
Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants
Authors:
Garcia, Maxime, Juhos, Szilveszter, Larsson, Malin, Olason, Pall I, Martin, Marcel, Eisfeldt, Jesper, DiLorenzo, Sebastian, Sandgren, Johanna, Díaz De Ståhl, Teresita, Ewels, Philip, Wirta, Valtteri, Nistér, Monica, Käller, Max, Nystedt, Björn
Publisher Information:
Linköpings universitet, Bioinformatik Linköpings universitet, Tekniska fakulteten Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Sweden Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Sweden; Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Sweden; Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Sweden Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Sweden Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Sweden Clinical Genetics, Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Sweden Department of Medical Sciences, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University,Sweden Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital at Solna, Sweden Department of Oncology-Pathology, Karolinska Institutet, J530 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Sweden Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Sweden Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Facility, Science for Life Laboratory, Karolinska Institutet, Sweden Department of Oncology-Pathology, Karolinska Institutet, J530 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Sweden School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Sweden Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Sweden F1000 Research Ltd 2020
Document Type:
E-Ressource Electronic Resource
Index Terms:
Analysis workflow; Cancer; Germline variants; Somatic variants; Whole Genome Sequencing, Genetics, Genetik, Article in journal, info:eu-repo/semantics/article, text
DOI:
10.12688.f1000research.16665.2
URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-174221
Availability:
Open access content. Open access content
info:eu-repo/semantics/openAccess
Note:
application/pdf
English
Other Numbers:
UPE oai:DiVA.org:liu-174221
doi:10.12688/f1000research.16665.2
PMID 32269765
1248682972
Contributing Source:
UPPSALA UNIV LIBR
From OAIster®, provided by the OCLC Cooperative.
Accession Number:
edsoai.on1248682972
Database:
OAIster

Weitere Informationen

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/.