omicverse.alignment.vsearch.sintax

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omicverse.alignment.vsearch.sintax#

omicverse.alignment.vsearch.sintax(asvs_fasta, db_fasta, output_dir, cutoff=0.8, strand='both', threads=4, extra_args=None, vsearch_path=None, auto_install=True, overwrite=False)[source]#

Taxonomy assignment via SINTAX.

Parameters:

  • asvs_fasta (str) – Query ASV FASTA.

  • db_fasta (str) – Required path to a SINTAX-formatted reference FASTA (headers must encode taxonomy as ;tax=d:...,p:...,c:...;). Must be explicitly provided — no $HOME fallback. See omicverse.alignment.fetch_silva().

  • cutoff (float (default: 0.8)) – Bootstrap confidence threshold (default 0.8). Stored in SINTAX output as two columns: raw classifications and cutoff-filtered classifications.

  • strand (str (default: 'both')) – plus | minus | both.

  • output_dir (str)

  • 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))

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