omicverse.alignment.cutadapt

Contents

omicverse.alignment.cutadapt#

omicverse.alignment.cutadapt(samples, primer_fwd, primer_rev=None, output_dir='cutadapt', threads=4, jobs=None, output_gzip=None, discard_untrimmed=True, min_length=50, max_n=0, extra_args=None, cutadapt_path=None, auto_install=True, overwrite=False)[source]#

Run cutadapt to remove amplicon PCR primers.

Parameters:

  • samples (Union[Tuple[str, str, Optional[str]], Sequence[Tuple[str, str, Optional[str]]]]) – (sample, fq1, fq2) tuple, list of such tuples, or 1-2 FASTQ paths.

  • primer_fwd (str) – Forward primer sequence (5’ anchor on R1). IUPAC ambiguity allowed. Common 16S V4 choice: GTGYCAGCMGCCGCGGTAA (515F Parada).

  • primer_rev (Optional[str] (default: None)) – Reverse primer (5’ anchor on R2). For V4: GGACTACNVGGGTWTCTAAT (806R Apprill).

  • output_dir (str (default: 'cutadapt')) – Output directory; per-sample subdirs are created under it.

  • threads (int (default: 4)) – Threads per cutadapt invocation.

  • jobs (Optional[int] (default: None)) – Concurrent sample jobs (default: CPU/2, capped by sample count).

  • output_gzip (Optional[bool] (default: None)) – Force gzipped output; None follows input suffix.

  • discard_untrimmed (bool (default: True)) – Drop read pairs where primers were not found (standard for 16S).

  • min_length (int (default: 50)) – Minimum post-trim length; pairs shorter than this are dropped.

  • max_n (Optional[int] (default: 0)) – Maximum ambiguous bases allowed per read (None disables filter).

  • extra_args (Optional[Sequence[str]] (default: None)) – Additional cutadapt CLI arguments appended verbatim.

  • cutadapt_path (Optional[str] (default: None)) – Explicit path to cutadapt executable.

  • auto_install (bool (default: True)) – Try to install via conda when missing.

  • overwrite (bool (default: False)) – Re-run and overwrite existing outputs.

Return type:

Union[Dict[str, str], List[Dict[str, str]]]

Contents