omicverse.alignment.vsearch.usearch_global

omicverse.alignment.vsearch.usearch_global(reads_fasta, asvs_fasta, output_dir, identity=0.97, threads=4, strand='plus', extra_args=None, vsearch_path=None, auto_install=True, overwrite=False)

Build the ASV count matrix.

reads_fasta is typically the concatenated filtered FASTA (with <sample>.<n> headers) from dereplicate() (output combined). Each read is mapped to the closest ASV at identity (default 0.97) and tallied per sample.

Output

otutab.tsv — tab-delimited; first column #OTU ID, subsequent columns one per sample, rows = ASVs.

param reads_fasta:

type reads_fasta:

str

param asvs_fasta:

type asvs_fasta:

str

param output_dir:

type output_dir:

str

param identity:

type identity:

float (default: 0.97)

param threads:

type threads:

int (default: 4)

param strand:

type strand:

str (default: 'plus')

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)