Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
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.
iii. Download the pipeline and test it on a minimal dataset with a single command
nextflow run nf-core/sarek -profile test,<docker/singularity/conda/institute>
Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute.
If so, you can simply use
-profile <institute>in your command.
This will enable either
singularityand set the appropriate execution settings for your local compute environment.
iv. Start running your own analysis!
nextflow run nf-core/sarek -profile <docker/singularity/conda/institute> --input '\*.tsv' --genome GRCh38
See usage docs for all of the available options when running the pipeline.
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
* Extra documentation on variant calling
* Complementary information about ASCAT
* Complementary information about Sentieon
* 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).
* Adrian Lärkeryd
* Alexander Peltzer
* Chela James
* David Mas-Ponte
* Francesco L
* Friederike Hanssen
* Gisela Gabernet
* Harshil Patel
* James A. Fellows Yates
* Jesper Eisfeldt
* Johannes Alneberg
* Lucia Conde
* Malin Larsson
* Marcel Martin
* Nilesh Tawari
* Olga Botvinnik
* Phil Ewels
* Sabrina Krakau
* Tobias Koch
* Winni Kretzschmar
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 article as follows:
Garcia M, Juhos S, Larsson M et al. *Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 1; peer review: 2 approved]* *F1000Research* 2020, 9:63 doi: 10.12688/f1000research.16665.1.
You can cite the sarek zenodo record for a specific version using the following doi: 10.5281/zenodo.3476426
You can cite the
nf-core publication as follows:
*The nf-core framework for community-curated bioinformatics pipelines.*
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.