Primer detection and removal
Many basecalling and de-multiplexing tools do not remove primers from the amplicon sequences (but see Minibar (Krehenwinkel et al., 2019a)). NGSpeciesID, therefore, implements an optional primer removal step by searching the forward and reverse complement of each primer within a window at each end of the read. This is carried out for the polished sequences. If no primer is found, the polished consensus sequence(s) remain the final output of NGSpeciesID. If primer(s) have been detected and trimmed, NGSpeciesID reruns the reverse-complement removal and polishing steps to identify any remaining redundant consensus sequences that were not removed due to primers.