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.