The taxonomic affiliation tool from the FROGS pipeline is designed to assign taxonomy to the seed sequence of each ASV (Amplicon Sequence Variant). It integrates external tools such as RDPtools and BLAST to provide robust and reliable taxonomic annotations. These annotations are then added to the BIOM file and can be summarized into an HTML report for visualization. This step is essential to link the ASV sequences obtained after clustering and chimera removal to their potential biological identity, making downstream ecological and microbiome analyses possible.

The tool requires three main inputs: a reference database (pre-formatted and BLAST-indexed FASTA), a BIOM file containing ASV abundance data, and a FASTA file of ASV seed sequences. It then performs taxonomic assignment using either BLAST alignment against the reference database or the RDP classifier (if specified). Depending on the configuration, it can store a single taxonomy, a consensus taxonomy, or a list of possible taxonomies, along with optional metadata such as bootstrap values, alignment identity, and coverage. The output consists of a new BIOM file enriched with taxonomic affiliations, an HTML report with graphical summaries of the taxonomy distribution, and a log file documenting the commands executed. These results provide a structured and reproducible way to connect ASVs to their taxonomic classification.