ITS_assignment          Complete Fungal Assignment Pipeline
best_hit_taxonomy_assignment
                        Hierarchical best-hit taxonomy assignment with
                        per-rank fallback rule
check_N                 Check proportion of N bases in each sequence.
consensus_taxonomy_assignment
                        Per-rank consensus filter for taxonomy
                        assignment
easy_assignments        Easy taxonomy assignment for OTUs using BLAST
                        QC output & phylum-specific thresholds.
ensure_cols             Ensure data frame has all required columns (as
                        character)
load_and_check          Load and check BLAST results and rep-seq FASTA
parse_taxonomy_cutoffs
                        Parse taxonomy cutoffs file
plot_alignment_hist     Create and return alignment length histogram
                        (ggplot object)
safe_rbind_list         Safely rbinds list of data frames, ensuring
                        columns match
save_taxonomy_graphics
                        Save taxonomy summary charts and tables to
                        multi-page PDF
trim_alignments         Trim BLAST alignments by minimum length
write_initial_assignments
                        Create and write the initial assignments table
                        including drops at all steps
