Results indicated a slightly greater alignment rate (Fig. 1A, byPrim), reduced error rate (Fig. 1B), and a similar accuracy (Fig. 1C) compared with other HISAT2-based methods. However, the script is slightly simpler, with less ambiguity (for example, there are no reads excluded for matching alignment scores). Based on these evaluations, byPrim was judged to be optimal among the alignment methods.
