Snakemake workflow: microsatellite-instability-detection-with-msisensor-pro

A Snakemake workflow for microsatellite instability (MSI) detection with msisensor-pro, following best practices for standardized workflows.

• Snakemake workflow: microsatellite-instability-detection-with-msisensor-pro
  • Usage
  • Deployment options
  • Authors
  • References

Usage

The usage of this workflow is described in the Snakemake Workflow Catalog.

Detailed information about input data and workflow configuration can also be found in the config/README.md.

If you use this workflow in a paper, don't forget to give credits to the authors of this workflow and the tools it uses by citing:

1. The URL of this repository or its DOI.
2. The papers listed under References. Please also note that the main tool used here, msisensor-pro, is only free for non-commercial use by academic, government, and non-profit/not-for-profit institutionsfree to use by. For details and contact information for commercial licensing, see the msisensor-pro license.

Deployment options

To run the workflow from command line, change the working directory.

cd path/to/snakemake-workflow-name

Adjust options in the default config file config/config.yaml. Before running the complete workflow, you can perform a dry run using:

snakemake --dry-run

To run the workflow with test files using conda:

snakemake --cores 2 --sdm conda --directory .test

Authors

• David Lähnemann
  • German Cancer Consortium (DKTK), partner site Essen-Düsseldorf, A partnership between DKFZ and University Hospital Essen
  • https://orcid.org/0000-0002-9138-4112

References

Peng Jia, Xiaofei Yang, Li Guo, Bowen Liu, Jiadong Lin, Hao Liang, Jianyong Sun, Chengsheng Zhang, Kai Ye, MSIsensor-Pro: Fast, Accurate, and Matched-Normal-Sample-Free Detection of Microsatellite Instability, Genomics, Proteomics & Bioinformatics, Volume 18, Issue 1, February 2020, Pages 65–71, https://doi.org/10.1016/j.gpb.2020.02.001

Köster, J., Mölder, F., Jablonski, K. P., Letcher, B., Hall, M. B., Tomkins-Tinch, C. H., Sochat, V., Forster, J., Lee, S., Twardziok, S. O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., & Nahnsen, S. Sustainable data analysis with Snakemake. F1000Research, 10:33, 10, 33, 2021. https://doi.org/10.12688/f1000research.29032.2.

TODO

• Do not forget to also adjust the configuration-specific config/README.md file.