Sustainable data analysis with Snakemake

Mölder, Felix and Jablonski, Kim Philipp and Letcher, Brice and Hall, Michael B. and Tomkins-Tinch, Christopher H. and Sochat, Vanessa and Forster, Jan and Lee, Soohyun and Twardziok, Sven O. and Kanitz, Alexander and Wilm, Andreas and Holtgrewe, Manuel and Rahmann, Sven and Nahnsen, Sven and Köster, Johannes. (2021) Sustainable data analysis with Snakemake. F1000Research, 10. p. 33.

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Official URL: https://edoc.unibas.ch/85164/

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Data analysis often entails a multitude of heterogeneous steps, from the application of various command line tools to the usage of scripting languages like R or Python for the generation of plots and tables. It is widely recognized that data analyses should ideally be conducted in a reproducible way. Reproducibility enables technical validation and regeneration of results on the original or even new data. However, reproducibility alone is by no means sufficient to deliver an analysis that is of lasting impact (i.e., sustainable) for the field, or even just one research group. We postulate that it is equally important to ensure adaptability and transparency. The former describes the ability to modify the analysis to answer extended or slightly different research questions. The latter describes the ability to understand the analysis in order to judge whether it is not only technically, but methodologically valid. Here, we analyze the properties needed for a data analysis to become reproducible, adaptable, and transparent. We show how the popular workflow management system Snakemake can be used to guarantee this, and how it enables an ergonomic, combined, unified representation of all steps involved in data analysis, ranging from raw data processing, to quality control and fine-grained, interactive exploration and plotting of final results.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (Zavolan)
UniBasel Contributors:Kanitz, Alexander
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:F1000 Research Ltd.
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:23 Nov 2021 11:06
Deposited On:23 Nov 2021 11:06

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