skrakau/sarek

Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing

An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing

Introduction

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.

It's listed on the Elixir - Tools and Data Services Registry, Dockstore and omicX - Bioinformatics tools.

Documentation

The nf-core/sarek pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation
2. Pipeline configuration
   • Local installation
   • Adding your own system config
   • Install on a secure cluster
   • Reference genomes
   • Extra documentation on reference
3. Running the pipeline
   • Examples
   • Input files documentation
   • Documentation about containers
4. Output and how to interpret the results
   • Complementary information about ASCAT
   • Extra documentation on annotation
5. 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:

• Maxime Garcia
• Szilveszter Juhos

Helpful contributors:

• Johannes Alneberg
• Phil Ewels
• Jesper Eisfeldt
• Malin Larsson
• Marcel Martin
• Alexander Peltzer
• Nilesh Tawari
• arontommi
• bjornnystedt
• gulfshores
• KochTobi
• pallolason
• Sebastian-D
• 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

• CHANGELOG

Aknowledgements

Citation

If you use nf-core/sarek for your analysis, please cite the Sarek pre-print 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: awaiting peer review].. 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.
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