WITOD

WITOD analyzes within-taxon operational taxonomic unit (OTU) diversity in 16S rRNA amplicon microbiome datasets by identifying non-redundant sequence variants, refining taxonomy, and quantifying intra-taxon diversity.

Key Features:

• Alignment and Non-Redundancy: Aligns all OTU sequences within each taxon to produce non-redundant alignments and identify consensus regions at both ends leveraging conserved 16S rRNA regions.
• Relative Abundance Aggregation and Taxonomy Refinement: Combines relative abundance of identical OTUs and refines taxonomic assignments by performing BLASTn searches against the Silva database.
• Output Generation: Outputs an OTU table with unique OTUs, updated taxonomy, and combined relative abundances, and a diversity table linking the number of OTUs per taxon to their relative abundance in samples.

Scientific Applications:

• Genetic Polymorphism Analysis: Reveals intra-taxon genetic variants and lineages detectable in 16S rRNA amplicons to support analyses of microbiome-associated traits.
• Pathogen Identification: Assists identification of potential human pathogens or environmental disease vectors by uncovering hidden within-taxon diversity.
• Environmental Studies: Enables investigation of how varying within-taxon diversity correlates with environmental contexts using the diversity table.

Methodology:

WITOD is a Python-based program that requires an OTU table and a representative sequence file (rep_set.fna) in the same directory and implements within-taxon sequence alignment, BLASTn-based taxonomy refinement against the Silva database, and generation of OTU and diversity tables.