A binning tool to reconstruct viral haplotypes from assembled contigs

Jiao Chen; Jiayu Shang; Jianrong Wang; Yanni Sun

In practice though, the assumptions about the contigs' properties are not always true. Thus, in our implementation, we will use the consensus window depth as the number of haplotypes, by assuming that most windows cover all haplotypes and contain haplotype-specific mutations. For the contigs shown in Fig. 2 .(c), window depth 3 is the most frequent one. at three locations. Line weights represent the haplotype abundance. S 1 and S 2 are two mutation-free regions common to three haplotypes. S 1 and S 2 are at least 1k bp. (b): The alignment of contigs that satisfy the ideal condition. The grey-scale intensity represents the coverage of a contig. Three windows are produced. (c): The contigs that cannot cover all the three haplotypes. There are six windows. Their depth values are denoted below each window. For contig marked with "A S 2 ", its sequencing coverage is plotted above the contig.