uap: reproducible and robust HTS data analysis.

Autor: Kämpf C; Young Investigators Group Bioinformatics and Transcriptomics, Department Molecular Systems Biology, Helmholtz Center for Environmental Research - UFZ, Permoserstraße 15, Leipzig, 04318, Germany.; Bioinformatics Department, Universität Leipzig, Härtelstraße 16-18, Leipzig, 04107, Germany.; Bioinformatics Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, Leipzig, 04103, Germany.; Present address: Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, Leipzig, 04103, Germany., Specht M; Bioinformatics Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, Leipzig, 04103, Germany., Scholz A; Bioinformatics Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, Leipzig, 04103, Germany., Puppel SH; Bioinformatics Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, Leipzig, 04103, Germany., Doose G; Bioinformatics Department, Universität Leipzig, Härtelstraße 16-18, Leipzig, 04107, Germany.; Present address: ecSeq Bioinformatics GmbH, Sternwartenstraße 29, Leipzig, 04103, Germany., Reiche K; Bioinformatics Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, Leipzig, 04103, Germany., Schor J; Young Investigators Group Bioinformatics and Transcriptomics, Department Molecular Systems Biology, Helmholtz Center for Environmental Research - UFZ, Permoserstraße 15, Leipzig, 04318, Germany. jana.schor@ufz.de., Hackermüller J; Young Investigators Group Bioinformatics and Transcriptomics, Department Molecular Systems Biology, Helmholtz Center for Environmental Research - UFZ, Permoserstraße 15, Leipzig, 04318, Germany. joerg.hackermueller@ufz.de.; Bioinformatics Department, Universität Leipzig, Härtelstraße 16-18, Leipzig, 04107, Germany. joerg.hackermueller@ufz.de.
Jazyk: angličtina
Zdroj: BMC bioinformatics [BMC Bioinformatics] 2019 Dec 12; Vol. 20 (1), pp. 664. Date of Electronic Publication: 2019 Dec 12.
DOI: 10.1186/s12859-019-3219-1
Abstrakt: Background: A lack of reproducibility has been repeatedly criticized in computational research. High throughput sequencing (HTS) data analysis is a complex multi-step process. For most of the steps a range of bioinformatic tools is available and for most tools manifold parameters need to be set. Due to this complexity, HTS data analysis is particularly prone to reproducibility and consistency issues. We have defined four criteria that in our opinion ensure a minimal degree of reproducible research for HTS data analysis. A series of workflow management systems is available for assisting complex multi-step data analyses. However, to the best of our knowledge, none of the currently available work flow management systems satisfies all four criteria for reproducible HTS analysis.
Results: Here we present uap, a workflow management system dedicated to robust, consistent, and reproducible HTS data analysis. uap is optimized for the application to omics data, but can be easily extended to other complex analyses. It is available under the GNU GPL v3 license at https://github.com/yigbt/uap.
Conclusions: uap is a freely available tool that enables researchers to easily adhere to reproducible research principles for HTS data analyses.
Databáze: MEDLINE
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