ITS_assignment: Complete Fungal Assignment Pipeline

In ClassifyITS: Fungal Assignment Pipeline

Complete Fungal Assignment Pipeline

Description

Runs all steps: QC, filtering, plotting, assignments; optionally writes outputs.

Usage

ITS_assignment(
  blast_file,
  rep_fasta,
  cutoffs_file = NULL,
  cutoff_fraction = 0.6,
  n_cutoff = 1,
  outdir = NULL,
  verbose = FALSE
)

Arguments

blast_file	Path to BLAST results TSV file
rep_fasta	Path to representative sequences FASTA file
cutoffs_file	Path to taxonomy cutoffs CSV file (optional; defaults to package example if omitted)
cutoff_fraction	Numeric, fraction of median rep-seq length for BLAST filtering (default: 0.6)
n_cutoff	Numeric, N base percentage cutoff (default: 1)
outdir	Output directory for results. If NULL (default), nothing is written.
verbose	Logical; if TRUE emit progress messages. Default FALSE.

Value

Named list of results and (if written) output file paths

ClassifyITS documentation built on April 9, 2026, 5:08 p.m.