(3) Re-assembly and soft boundary
During the subsequent assembly or re-assembly processes, the accuracy of the bases gradually diminishes as the extension length along both sides of the recovered target gene increases. However, this decline is not sudden but rather a gradual decrease within a certain buffer length. To address this, we introduced a compensation mechanism called soft boundary. Soft boundary is a vague boundary between the regions with low and high read coverage; this buffer ensures that the accuracy of phylogenetic information remains relatively stable with only subtle changes in its edge. To support maximum performance of the program, we suggest setting the soft boundary to half the read length.