Detect Primer Dimers in Amplicon Sequences

This function identifies potential primer dimers in paired-end sequencing data based on sequence length and primer matching criteria.

detect_primer_dimer(
  reads_df,
  forward_primer,
  reverse_primer,
  max_dimer_length = 100,
  min_match_score = -40
)

Arguments

reads_df

A data frame from parse_fastq_pairs containing read pairs

forward_primer

Character string of the forward primer sequence

reverse_primer

Character string of the reverse primer sequence

max_dimer_length

Maximum length for primer dimer classification (default: 100)

min_match_score

Minimum primer to read alignment score. Based on gap penalty need for alignemtn (gap opening = -10, gap extension = -4; default: -40)

Value

A logical vector indicating which reads are classified as primer dimers