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WIP: An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing
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README.md

Sarek

nf-core

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

⚠️ This pipeline is a work in progress being ported to nf-core from SciLifeLab/Sarek

Nextflow version nf-core

Travis build status CircleCi build status

Install with bioconda Docker Container available Install with Singularity

Join us on Slack

Introduction

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 including 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 is 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
  3. Running the pipeline
  4. Output and how to interpret the results
  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:

Helpful contributors:

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 or contact us: maxime.garcia@scilifelab.se, szilveszter.juhos@scilifelab.se

CHANGELOG

Aknowledgements

Barntumörbanken SciLifeLab
National Genomics Infrastructure National Bioinformatics Infrastructure Sweden
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