Fungal Assignment Pipeline

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Documentation for package ‘ClassifyITS’ version 1.0.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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)
ITS_assignment	Complete Fungal Assignment Pipeline
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