THAPBI PICT-a fast, cautious, and accurate metabarcoding analysis pipeline

Area of Science:

• Bioinformatics
• Genomics
• Computational Biology

Background:

• Metabarcoding analysis of environmental DNA (eDNA) is crucial for biodiversity assessment.
• Existing pipelines often require specialized configurations for different marker genes and organisms.
• Handling multiplexed amplicons and noisy sequence data presents analytical challenges.

Purpose of the Study:

• To introduce THAPBI PICT, a flexible open-source software pipeline for metabarcoding analysis.
• To demonstrate the adaptability of THAPBI PICT for diverse amplicons, organisms, and datasets beyond its initial scope.
• To provide a user-friendly tool for non-specialists to interpret metabarcoding results.

Main Methods:

• Data reduction to Amplicon Sequence Variants (ASVs) from Illumina paired-end reads.
• Application of dynamic abundance thresholds for noise and artifact removal.
• Classification of ASVs against curated reference databases with flexible matching criteria.

Main Results:

• THAPBI PICT successfully processes multiplexed samples and various amplicons with appropriate settings.
• The pipeline effectively identifies ASVs and classifies them based on user-defined or automated abundance thresholds.
• Generated outputs include detailed read and sample reports, along with ASV topological graphs for interpretation.

Conclusions:

• THAPBI PICT offers a robust and adaptable solution for metabarcoding analysis, enhancing accessibility for researchers.
• The software's modular design allows for broad application across different ecological and biological studies.
• Availability of source code and documentation facilitates widespread adoption and further development.