omicverse.alignment.vsearch.uchime3_denovo

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omicverse.alignment.vsearch.uchime3_denovo#

omicverse.alignment.vsearch.uchime3_denovo(asvs_fasta, output_dir, vsearch_path=None, auto_install=True, overwrite=False)[source]#

De novo chimera detection / removal on UNOISE3 ASVs.

Note that UNOISE3 already applies a lightweight chimera filter; running uchime3_denovo as a second pass is a conservative extra step.

Note

vsearch’s --uchime3_denovo is intentionally single-threaded upstream, so there is no threads= parameter (unlike the other wrappers in this module).

Parameters:

  • asvs_fasta (str)

  • output_dir (str)

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

  • auto_install (bool (default: True))

  • overwrite (bool (default: False))

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