RiboSnake - a user-friendly, robust, reproducible, multipurpose and documentation-extensive pipeline for 16S rRNA gene microbiome analysis.

Autor:	Dörr AK; Institute for Artificial Intelligence in Medicine, University Duisburg-Essen, 45131, Essen, Germany., Welling J; Institute for Artificial Intelligence in Medicine, University Duisburg-Essen, 45131, Essen, Germany., Dörr A; Institute for Artificial Intelligence in Medicine, University Duisburg-Essen, 45131, Essen, Germany., Gosch J; Institute for Artificial Intelligence in Medicine, University Duisburg-Essen, 45131, Essen, Germany., Möhlen H; Institute for Artificial Intelligence in Medicine, University Duisburg-Essen, 45131, Essen, Germany., Schmithausen R; Institute for Artificial Intelligence in Medicine, University Duisburg-Essen, 45131, Essen, Germany.; Institute for Hygiene and Public Health, University Hospital Bonn, 53127, Bonn, Germany., Kehrmann J; Institute for Medical Microbiology, University Hospital Essen, 45147, Essen, Germany., Meyer F; Institute for Artificial Intelligence in Medicine, University Duisburg-Essen, 45131, Essen, Germany., Kraiselburd I; Institute for Artificial Intelligence in Medicine, University Duisburg-Essen, 45131, Essen, Germany.
Jazyk:	angličtina
Zdroj:	GigaByte (Hong Kong, China) [GigaByte] 2024 Aug 31; Vol. 2024, pp. gigabyte132. Date of Electronic Publication: 2024 Aug 31 (Print Publication: 2024).
DOI:	10.46471/gigabyte.132
Abstrakt:	Background: Next-generation sequencing for microbial communities has become a standard technique. However, the computational analysis remains resource-intensive. With declining costs and growing adoption of sequencing-based methods in many fields, validated, fully automated, reproducible and flexible pipelines are increasingly essential in various scientific fields. Results: We present RiboSnake, a validated, automated, reproducible QIIME2-based pipeline implemented in Snakemake for analysing 16S rRNA gene amplicon sequencing data. RiboSnake includes pre-packaged validated parameter sets optimized for different sample types, from environmental samples to patient data. The configuration packages can be easily adapted and shared, requiring minimal user input. Conclusion: RiboSnake is a new alternative for researchers employing 16S rRNA gene amplicon sequencing and looking for a customizable and user-friendly pipeline for microbiome analyses with in vitro validated settings. By automating the analysis with validated parameters for diverse sample types, RiboSnake enhances existing methods significantly. The workflow repository can be found on GitHub (https://github.com/IKIM-Essen/RiboSnake). Competing Interests: The authors declare no competing interests. (© The Author(s) 2024.)
Databáze:	MEDLINE
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