A De Novo Genome Assembly Algorithm for Repeats and Nonrepeats
Figure 4
Schematic of extending repeats and boundary detection. The graphic illustration of extending repeats and boundary detection. Red line represents the extended repeats, blue line represents the extending repeats, and the green line represents the potential nonrepeats. The yellow lines represent the supporting reads overlapped with the extended contig. We assume that the sequencing depth , and let . Therefore, in the process of extending repeats, the mean value of dynamic overlapping interval filtered by sliding window as shown in Figure 2(d) should be larger than or equal to . The dotted box represents the potential boundary of repeats. Consequently, if we set , the extension will be stopped at B1 or the extension will be stopped at B2.
