TaxonTableTools

TaxonTableTools processes TaXon tables derived from read tables and taxonomy tables to perform taxonomic aggregation, visualization, and ecological metric calculation for DNA metabarcoding-based biodiversity assessment and regulatory bioassessment data formats.

Key Features:

• Input format - TaXon table: Accepts TaXon tables generated from read tables and taxonomy tables produced by established metabarcoding pipelines.
• Compatibility with metabarcoding pipelines: Supports import of sequence read data produced by various established metabarcoding pipelines via the TaXon table format.
• Venn diagrams: Computes Venn diagrams to compare taxon overlap among replicates, samples, or analytical methods.
• Read proportion statistics: Calculates read proportion per taxon and basic compositional statistics for datasets.
• Krona charts: Generates interactive Krona charts for hierarchical in-depth taxonomic data exploration.
• Alpha and beta diversity estimates: Computes alpha and beta diversity metrics for community-level diversity assessment.
• Rarefaction analysis: Performs rarefaction analysis to evaluate sampling effort and species accumulation.
• Ordination plots: Produces ordination plots for community composition and multivariate analysis.
• Regulatory data formats: Exports data formats required for traditional taxonomy-based analyses used in regulatory bioassessment programs.

Scientific Applications:

• Biodiversity assessment: Converts sequence read data into taxonomic summaries and metrics for DNA metabarcoding-based biodiversity studies.
• Taxonomic composition analysis: Supports analysis of taxonomic composition and relative abundance using read proportions and Krona visualizations.
• Community ecology and diversity analyses: Enables community ecology studies through alpha/beta diversity, rarefaction, and ordination analyses.
• Regulatory bioassessment and monitoring: Produces outputs compatible with taxonomy-based regulatory bioassessment workflows and monitoring programs.

Methodology:

Uses TaXon table input generated from read tables and taxonomy tables produced by metabarcoding pipelines and computes Venn diagrams, read proportion statistics, Krona charts, alpha and beta diversity estimates, rarefaction analyses, ordination plots, and exports regulatory-compatible taxonomy-based data formats.