omicverse.alignment.vsearch.filter_quality

omicverse.alignment.vsearch.filter_quality(merged, output_dir, max_ee=1.0, min_len=0, max_len=0, trunc_len=0, max_ns=0, threads=4, jobs=None, extra_args=None, vsearch_path=None, auto_install=True, overwrite=False)

Filter merged FASTQs and write per-sample FASTA with labels.

Accepts:

• list of dicts from merge_pairs() with keys sample and merged

• list of (sample, merged_path) tuples

• list of fastq paths (sample name derived from filename)

Output per sample: output_dir/<sample>/<sample>_filt.fasta with headers relabeled <sample>.<n> so downstream --otutabout can resolve sample identity from the read label prefix.

Parameters:

• merged (Union[Sequence[Dict[str, str]], Sequence[str], Sequence[Tuple[str, str]]])

• output_dir (str)

• max_ee (float (default: 1.0))

• min_len (int (default: 0))

• max_len (int (default: 0))

• trunc_len (int (default: 0))

• max_ns (int (default: 0))

• threads (int (default: 4))

• jobs (Optional[int] (default: None))

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

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

• auto_install (bool (default: True))

• overwrite (bool (default: False))