AmpliconTagger

AmpliconTagger processes ribosomal RNA (rRNA) gene amplicon sequencing data to generate operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) and to perform taxonomic classification and diversity analyses.

Key Features:

• Python Framework: Implemented in Python to enable integration with bioinformatics tools and libraries.
• HPC Compatibility: Optimized for high-performance computing (HPC) environments and supports complex job dependencies and a smart-restart mechanism.
• Customization and Flexibility: Provides extensive customization options and the ability to integrate stand-alone software packages.
• Integration of Diverse Algorithms: Supports algorithms for generating OTUs and ASVs and for computing taxonomic summaries and diversity metrics for 16S, 18S, and ITS amplicons.
• Support for Multiple Data Types: Processes short-read and long-read sequencing data, including Pacific Biosciences reads.

Scientific Applications:

• Phylogenetic Studies: Analysis of 16S, 18S, and ITS rRNA gene amplicons to infer microbial diversity and phylogeny.
• Microbial Ecology: Systematic analysis of microbial community composition and ecological interactions.
• Taxonomic Classification: Detailed taxonomic classification and diversity assessments using generated OTUs or ASVs.

Methodology:

Raw sequence input followed by quality control, alignment, clustering to generate OTUs or ASVs, and subsequent taxonomic classification and diversity analysis using published algorithms.