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Sarek - 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 designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses.

It’s built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Sarek was developed at the National Genomics Infastructure and National Bioinformatics Infastructure Sweden which are both platforms at SciLifeLab. It is listed on the Elixir – Tools and Data Services Registry.


Please refer to the sarek documentation on the nf-core website.

Contributions & Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don’t hesitate to get in touch on Slack or contact us: maxime.garcia@scilifelab.se, szilveszter.juhos@scilifelab.se




See the code for Sarek here: https://github.com/SciLifeLab/Sarek