qbicpipelines/sarek repository overview
An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing
Introduction
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.
It's listed on Elixir - Tools and Data Services Registry and Dockstore.
Quick Start
i. Install Nextflow
ii. Install either Docker or Singularity for full pipeline reproducibility (please only use Conda as a last resort; see docs)
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 eitherdockerorsingularityand 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.
Documentation
The nf-core/sarek pipeline comes with documentation about the pipeline, found in the docs/ directory:
- Installation
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
- Troubleshooting
Credits
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).
Main authors:
Helpful contributors:
- 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
- Sebastian-D
- Tobias Koch
- Winni Kretzschmar
- arontommi
- bjornnystedt
- cgpu
- gulfshores
- pallolason
- silviamorins
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 (you can join with this invite) or contact us: [email protected], [email protected]
CHANGELOG
Acknowledgements
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Citation
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.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
ReadCube: Full Access Link
Tag summary
Content type
Image
Digest
Size
1.6 GB
Last updated
over 6 years ago
docker pull qbicpipelines/sarek