FROGS

FROGS generates and analyzes operational taxonomic units (OTUs) from DNA amplicon sequences to characterize microbial and fungal community composition in metabarcoding studies.

Key Features:

• Operational Taxonomic Unit (OTU) Analysis: Generates OTU abundance tables with taxonomic affiliations using Swarm for clustering.
• Chimera Removal and Validation: Employs VSEARCH for chimera detection and removal combined with a cross-sample validation method.
• Multi-Affiliation Taxonomic Output: Produces multi-affiliation outputs that highlight taxonomic conflicts and uncertainties across different databases.
• Statistical and Graphical Outputs: Produces statistical results and graphical illustrations to summarize and monitor analyses.
• Performance Benchmarking: Tested on real and simulated datasets with reported rapid processing, robustness, high sensitivity, and comparable or superior performance to mothur, UPARSE, and QIIME.
• Fungal Metabarcoding (ITS): Accommodates both overlapping and non-overlapping reads from ITS markers to improve representation of fungal communities.

Scientific Applications:

• Microbial Ecology: Profiling microbial community composition using OTU abundance tables and taxonomic assignments.
• Fungal Community Studies and Food Industry Applications: Metabarcoding of fungal communities with ITS read handling to support ecological assessment and food-related analyses.
• Method Benchmarking and Comparative Studies: Comparative evaluation of metabarcoding workflows and sensitivity against tools such as mothur, UPARSE, and QIIME.

Methodology:

Clustering with Swarm to produce OTUs and abundance tables; chimera detection and removal with VSEARCH including cross-sample validation; taxonomic assignment producing multi-affiliation outputs across databases; generation of statistical metrics and graphical illustrations; accommodation of overlapping and non-overlapping ITS reads.