omicverse.alignment.vsearch.dereplicate

omicverse.alignment.vsearch.dereplicate(filtered, output_dir, min_uniq=2, threads=4, extra_args=None, vsearch_path=None, auto_install=True, overwrite=False)

Combine + dereplicate filtered FASTAs → one uniques.fasta.

The concatenated file combined.fasta is also written; downstream usearch_global() uses it to build the sample × ASV count matrix because it preserves per-read sample labels.

Parameters:

• filtered (Union[Sequence[Dict[str, str]], Sequence[str]])

• output_dir (str)

• min_uniq (int (default: 2))

• threads (int (default: 4))

• extra_args (Optional[Sequence[str]] (default: None))

• vsearch_path (Optional[str] (default: None))

• auto_install (bool (default: True))

• overwrite (bool (default: False))