OTUbase: an R infrastructure package for operational taxonomic unit data

Area of Science:

• Bioinformatics
• Computational Biology
• Microbial Ecology

Background:

• Existing software clusters sequence data into operational taxonomic units (OTUs) or classifies sequences taxonomically.
• There is a need for tools to organize and manage the summarized outputs from these bioinformatics pipelines.
• Researchers require accessible formats for downstream analysis of microbial community data.

Purpose of the Study:

• To introduce OTUbase, an R package designed for the analysis of OTU and taxonomic sequence data.
• To provide a structured format for summarized outputs from sequence analysis pipelines.
• To facilitate data manipulation and further analysis using the R ecosystem.

Main Methods:

• Development of an R package named OTUbase.
• Implementation of data structures for organizing OTU and taxonomic data.
• Leveraging the capabilities of the R statistical environment and its associated packages.

Main Results:

• OTUbase provides a structured framework for handling OTU and taxonomic data within R.
• The package facilitates easy access and manipulation of summarized sequence analysis outputs.
• Researchers can readily integrate OTUbase with other R packages for advanced analyses.

Conclusions:

• OTUbase enhances the analysis of microbial community composition data.
• The package streamlines the workflow for researchers working with large-scale sequence data.
• OTUbase empowers researchers to perform complex analyses on OTU and taxonomic data efficiently.