RiboSnake - a User-friendly, Robust, Reproducible, Multipurpose and Documentation-extensive Pipeline for 16S RRNA Gene Microbiome Analysis

Overview

Journal GigaByte

Date 2024 Oct 4

PMID 39364224

Authors

Ann-Kathrin Dorr

Josefa Welling

Adrian Dorr

Jule Gosch

Hannah Mohlen

Ricarda Schmithausen

Jan Kehrmann

Folker Meyer

Ivana Kraiselburd

Affiliations

Soon will be listed here.

Abstract

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 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 gene amplicon sequencing and looking for a customizable and user-friendly pipeline for microbiome analyses with 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).

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