Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
nf-core/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.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website.
Depending on the options and samples provided, the pipeline can currently perform the following:
- Form consensus reads from UMI sequences (
- Sequencing quality control and trimming (
- Map Reads to Reference (
- Process BAM file (
- Summarise alignment statistics (
- Variant calling (enabled by
--tools, see compatibility):
- Variant filtering and annotation (
- Summarise and represent QC (
First, prepare a samplesheet with your input data that looks as follows:
Each row represents a pair of fastq files (paired end).
Now, you can run the pipeline using:
See usage docs for all of the available options when running the pipeline.
Warning: Please provide pipeline parameters via the CLI or Nextflow
-params-fileoption. Custom config files including those provided by the
-cNextflow option can be used to provide any configuration except for parameters; see docs.
To see the the results of a test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.
Sarek was originally written by Maxime U Garcia and Szilveszter Juhos 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). Friederike Hanssen and Gisela Gabernet at QBiC later joined and helped with further development.
The Nextflow DSL2 conversion of the pipeline was lead by Friederike Hanssen and Maxime U Garcia.
Maintenance is now lead by Friederike Hanssen and Maxime U Garcia (now at Seqera Labs)
We thank the following people for their extensive assistance in the development of this pipeline:
- Abhinav Sharma
- Adam Talbot
- Adrian Lärkeryd
- Alexander Peltzer
- Anders Sune Pedersen
- Chela James
- David Mas-Ponte
- Francesco Lescai
- Gavin Mackenzie
- Gisela Gabernet
- Harshil Patel
- James A. Fellows Yates
- Jesper Eisfeldt
- Johannes Alneberg
- José Fernández Navarro
- Lasse Westergaard Folkersen
- Lucia Conde
- Malin Larsson
- Marcel Martin
- Nick Smith
- Nilesh Tawari
- Olga Botvinnik
- Oskar Wacker
- Paul Cantalupo
- Phil Ewels
- Sabrina Krakau
- Silvia Morini
- Solenne Correard
- Susanne Jodoin
- Szilveszter Juhos
- Tobias Koch
- Winni Kretzschmar
- Alison Meynert
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 2; peer review: 2 approved] F1000Research 2020, 9:63 doi: 10.12688/f1000research.16665.2.
You can cite the sarek zenodo record for a specific version using the following doi: 10.5281/zenodo.3476425
An extensive list of references for the tools used by the pipeline can be found in the
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.