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ZARP: An automated workflow for processing of RNA-seq data

View ORCID ProfileMaria Katsantoni, View ORCID ProfileFoivos Gypas, View ORCID ProfileChristina J. Herrmann, View ORCID ProfileDominik Burri, View ORCID ProfileMaciej Bak, View ORCID ProfilePaula Iborra, View ORCID ProfileKrish Agarwal, View ORCID ProfileMeric Ataman, View ORCID ProfileAnastasiya Börsch, View ORCID ProfileMihaela Zavolan, View ORCID ProfileAlexander Kanitz
doi: https://doi.org/10.1101/2021.11.18.469017
Maria Katsantoni
1Biozentrum, University of Basel, Basel, 4056, Switzerland
2Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
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  • ORCID record for Maria Katsantoni
Foivos Gypas
3Friedrich Miescher Institute for Biomedical Research, Basel, 4058, Switzerland
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  • ORCID record for Foivos Gypas
Christina J. Herrmann
1Biozentrum, University of Basel, Basel, 4056, Switzerland
2Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
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Dominik Burri
1Biozentrum, University of Basel, Basel, 4056, Switzerland
2Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
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Maciej Bak
1Biozentrum, University of Basel, Basel, 4056, Switzerland
2Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
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  • ORCID record for Maciej Bak
Paula Iborra
1Biozentrum, University of Basel, Basel, 4056, Switzerland
2Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
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Krish Agarwal
1Biozentrum, University of Basel, Basel, 4056, Switzerland
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  • ORCID record for Krish Agarwal
Meric Ataman
1Biozentrum, University of Basel, Basel, 4056, Switzerland
2Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
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Anastasiya Börsch
1Biozentrum, University of Basel, Basel, 4056, Switzerland
2Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
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Mihaela Zavolan
1Biozentrum, University of Basel, Basel, 4056, Switzerland
2Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
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  • For correspondence: alexander.kanitz@unibas.ch
Alexander Kanitz
1Biozentrum, University of Basel, Basel, 4056, Switzerland
2Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
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  • ORCID record for Alexander Kanitz
  • For correspondence: alexander.kanitz@unibas.ch
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Abstract

RNA sequencing (RNA-seq) is a crucial technique for many scientific studies and multiple models, and software packages have been developed for the processing and analysis of such data. Given the plethora of available tools, choosing the most appropriate ones is a time-consuming process that requires an in-depth understanding of the data, as well as of the principles and parameters of each tool. In addition, packages designed for individual tasks are developed in different programming languages and have dependencies of various degrees of complexity, which renders their installation and execution challenging for users with limited computational expertise. The use of workflow languages and execution engines with support for virtualization and encapsulation options such as containers and Conda environments facilitates these tasks considerably. Computational workflows defined in those languages can be reliably shared with the scientific community, enhancing reusability, while improving reproducibility of results by making individual analysis steps more transparent.

Here we present ZARP, a general purpose RNA-seq analysis workflow which builds on state-of-the-art software in the field to facilitate the analysis of RNA-seq data sets. ZARP is developed in the Snakemake workflow language using best software development practices. It can run locally or in a cluster environment, generating extensive reports not only of the data but also of the options utilized. It is built using modern technologies with the ultimate goal to reduce the hands-on time for bioinformaticians and non-expert users. ZARP is available under a permissive Open Source license and open to contributions by the scientific community.

Contact mihaela.zavolan{at}unibas.ch, alexander.kanitz{at}unibas.ch

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/zavolanlab/zarp

  • https://zenodo.org/record/5703358

  • https://zenodo.org/record/5683524

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted November 19, 2021.
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ZARP: An automated workflow for processing of RNA-seq data
Maria Katsantoni, Foivos Gypas, Christina J. Herrmann, Dominik Burri, Maciej Bak, Paula Iborra, Krish Agarwal, Meric Ataman, Anastasiya Börsch, Mihaela Zavolan, Alexander Kanitz
bioRxiv 2021.11.18.469017; doi: https://doi.org/10.1101/2021.11.18.469017
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ZARP: An automated workflow for processing of RNA-seq data
Maria Katsantoni, Foivos Gypas, Christina J. Herrmann, Dominik Burri, Maciej Bak, Paula Iborra, Krish Agarwal, Meric Ataman, Anastasiya Börsch, Mihaela Zavolan, Alexander Kanitz
bioRxiv 2021.11.18.469017; doi: https://doi.org/10.1101/2021.11.18.469017

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