Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb

Area of Science:

• Biodiversity research
• Molecular ecology
• Bioinformatics

Background:

• DNA barcoding and metabarcoding rely on accurate reference databases for taxonomic assignment.
• Current methods using spreadsheets for database management are insufficient for large datasets and prone to errors.
• There is a need for user-friendly tools to manage DNA reference libraries efficiently.

Purpose of the Study:

• Introduce the R package refdb for constructing and managing DNA reference libraries.
• Provide scientists with a reliable and powerful tool for handling biodiversity sequence data.
• Facilitate standardization and repeatability in DNA barcoding and metabarcoding studies.

Main Methods:

• Development of the refdb R package.
• Implementation of functions for importing, organizing, cleaning, filtering, auditing, and exporting data.
• Application in biodiversity and biomonitoring studies.

Main Results:

• refdb offers a semi-automatic and assisted approach to reference library construction.
• The package provides robust data manipulation and management capabilities.
• refdb can significantly accelerate the generation and handling of DNA reference databases.

Conclusions:

• The refdb package addresses the limitations of traditional methods for managing DNA reference data.
• It offers a powerful solution for enhancing the quality and efficiency of biodiversity research using DNA barcoding and metabarcoding.
• refdb promotes standardization and repeatability in molecular biodiversity assessments.