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rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis.

Sebastien Theil1, Etienne Rifa1

  • 1Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, F-15000, Aurillac, France.

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|February 4, 2021
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Summary

This study introduces rANOMALY, an R package for automated microbial community analysis using 16S and ITS sequencing data. It simplifies complex bioinformatics workflows, ensuring reproducible and accurate results from raw sequences to statistical validation.

Keywords:
16SITSR packageamplicon sequencingmetagenomicsmicrobial community

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Computational Biology

Background:

  • Bioinformatic tools for marker gene sequencing data analysis are rapidly evolving, posing challenges for integration.
  • Analyzing 16S and ITS amplicon sequencing data requires robust and up-to-date computational methods.

Purpose of the Study:

  • To present rANOMALY, an R package designed to automate and standardize the analysis of 16S and ITS amplicon sequencing data.
  • To provide a flexible and reproducible workflow for microbial community characterization and analysis.
  • To integrate the latest bioinformatics methods and statistical validation into a user-friendly package.

Main Methods:

  • Development of an R package (rANOMALY) automating data processing from raw fastq files to diversity and differential analysis.
  • Utilizes amplicon sequence variants (ASV) for microbial community characterization.
  • Incorporates advanced bioinformatics techniques including sequence tracking, control sample decontamination, and multiple reference database utilization for taxonomic annotation.

Main Results:

  • rANOMALY automates the entire analysis pipeline, ensuring reproducibility across projects.
  • The package offers comprehensive ecological analyses with advanced statistical tests and cross-validated differential analysis using four distinct methods.
  • Outputs include publication-ready figures and Rmarkdown integration for automated report generation.

Conclusions:

  • rANOMALY provides a powerful, customizable, and easy-to-install solution for microbial community analysis.
  • The package enhances reproducibility and efficiency in processing amplicon sequencing data.
  • It facilitates the integration of novel bioinformatics tools and statistical approaches for microbial ecology research.