Figure 3

Schematic diagram of assembly from 454 reads and the relationship of repeat contigs. A. The genome has four unique sections (1–4) and two repeats (R1 and R2). B. One repeat contig and four unique contigs were assembled. The reads coming from R1 and R2 was assembled into the same contig, resulting in twice the coverage of other contigs. Some reads at the end of the repeat contig consisted of only partial sequences, and the other parts of the reads are located in other contigs. C. We can obtain four linkage relationships of the repeat contigs depending on reads covering different contigs. Among them 2 and 3 reflect the correct linkage whereas 1 and 4 was incorrect. D. The relationship shown in C was displayed in ContigScape. 1S-1E represent contig1; 2S-2E represent contig2; 3S-3E represent contig3; 4S-4E represent contig4; RS-RE represent contigR; red coloring represents repeat contigs, dark blue coloring represents unique contigs. “S” represents the starting position of the contig and “E” represents the termination location of the contig. Num 1, Num 2, Num 3, Num 4 represent the number of reads connecting contig R and “1E”, “2S”, “3S”, and “4S”, respectively. Length1, length2, length3 and length4 represent the lengths of contig1, contig2, contig3 and contig4, respectively. The width of the green edge is proportional to their number.