(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.