Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Introduction<img align="right" title="CAW" src="https://raw.githubusercontent.com/nf-core/sarek/2.5///docs/images/CAW_logo.png">
Previously known as the Cancer Analysis Workflow (CAW),
Sarek is a workflow designed to run analyses on whole genome or targeted sequencing data from regular samples or tumour / normal pairs and could include additional relapses.
It's built using Nextflow,
a domain specific language for workflow building,
across multiple compute infrastructures in a very portable manner.
Software dependencies are handled using Conda, Docker or Singularity - environment/container technologies that provide excellent reproducibility and ease of use.
Thus making installation trivial and results highly reproducible.
The nf-core/sarek pipeline comes with documentation about the pipeline, found in the
- Pipeline configuration
* Local installation
* Adding your own system config
* Install on a secure cluster
* Reference genomes
* Extra documentation on reference
- Running the pipeline
* Input files documentation
* Documentation about containers
- Output and how to interpret the results
* Complementary information about ASCAT
* Extra documentation on annotation
Sarek was developed at the National Genomics Infastructure and National Bioinformatics Infastructure Sweden which are both platforms at SciLifeLab, with the support of The Swedish Childhood Tumor Biobank (Barntumörbanken).
* Johannes Alneberg
* Phil Ewels
* Jesper Eisfeldt
* Malin Larsson
* Marcel Martin
* Alexander Peltzer
* Nilesh Tawari
Contributions & Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
If you use nf-core/sarek for your analysis, please cite the
Sarek pre-print as follows:
Garcia MU, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, de Ståhl TD, Wirta V, Nistér M, Nystedt B, Käller M. *Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants*. *bioRxiv*. 2018. p. 316976. doi: 10.1101/316976.
You can cite the sarek zenodo record for a specific version using the following doi: 10.5281/zenodo.2582812
You can cite the
nf-core pre-print as follows:
Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. *nf-core: Community curated bioinformatics pipelines*. *bioRxiv*. 2019. p. 610741. doi: 10.1101/610741.