omicverse.alignment.dada2.filter_and_trim

omicverse.alignment.dada2.filter_and_trim(samples, output_dir, trunc_len=0, max_ee=2.0, trunc_q=2, min_len=20, max_n=0, overwrite=False)

Quality-trim each sample’s FASTQs to output_dir/<sample>/.

Accepts (sample, fq1, fq2) tuples; fq2 may be None (single-end).

Parameters:

• samples (Union[Tuple[str, str, Optional[str]], Sequence[Tuple[str, str, Optional[str]]]])

• output_dir (str)

• trunc_len (Union[int, Tuple[int, int]] (default: 0))

• max_ee (Union[float, Tuple[float, float]] (default: 2.0))

• trunc_q (int (default: 2))

• min_len (int (default: 20))

• max_n (int (default: 0))

• overwrite (bool (default: False))