omicverse.alignment.vsearch.unoise3

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omicverse.alignment.vsearch.unoise3#

omicverse.alignment.vsearch.unoise3(uniques_fasta, output_dir, alpha=2.0, minsize=2, threads=4, extra_args=None, vsearch_path=None, auto_install=True, overwrite=False)[source]#

Run UNOISE3 denoising to build ASVs (amplicon sequence variants).

Equivalent biological resolution to DADA2 ASVs per multiple benchmarks (Vestergaard 2024 ISME Comms); uses VSEARCH’s C implementation of the UNOISE3 algorithm (--cluster_unoise).

Output#

asvs_pre.fasta — raw ASV centroids (pre-chimera removal).

param uniques_fasta:

type uniques_fasta:

str

param output_dir:

type output_dir:

str

param alpha:

type alpha:

float (default: 2.0)

param minsize:

type minsize:

int (default: 2)

param threads:

type threads:

int (default: 4)

param extra_args:

type extra_args:

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

param vsearch_path:

type vsearch_path:

Optional[str] (default: None)

param auto_install:

type auto_install:

bool (default: True)

param overwrite:

type overwrite:

bool (default: False)

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