An open-source analysis pipeline to detect germline or somatic variants from whole genome sequencing.
Previously known as the Cancer Analysis Workflow (CAW), Sarek is a workflow tool designed to run analyses on WGS data from regular samples or tumour / normal pairs, including relapse samples if required.
It’s built using Nextflow, a bioinformatics domain specific language for workflow building. Singularity has been designed specifically for high-performance computing environments. This means that although Sarek has been primarily designed for use with the Swedish UPPMAX HPC systems, it should be able to run on any system that supports these two tools.