Search and remove primer sequences — do_primer

Requires seqtool v0.4 or higher

See do_trim_demux for more details on the arguments

Usage

do_primer_search(
  fq_paths,
  amplicon_primers,
  out_dir,
  primer_max_err = 0.2,
  idx_max_diffs = 0,
  min_barcode_length = 50,
  cores = NULL
)

Value

Returns trimmed FASTQ paths (Zstandard-compressed) and statistics: list(trimmed_fq = c(...), stats = list(...)). More FASTQ files are generated for reads without primers/indexes or reads that are too short or potential concatenated products.

Details

The function generates different FASTQ files in out_dir, whereby trimmed.fastq.zst contains "valid" reads with sample indexes in the sequence headers: <id> fi=<fwd-idx-name> ri=<rev-idx-name>