Fig. 4
From: Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph
Overall pipeline of nanoGapFiller. Step 1. Initially, nanoGapFiller aligns genome assembly contigs onto optical maps. The aligned contigs are further connected into scaffolds according to their order in the alignment. Note that some regions of optical maps often fail to align with any contig, thus forming gaps in scaffolds. Here, we identified a gap with site sequence \(x_3 x_4 x_5 x_6\). Step 2. To fill this gap, nanoGapFiller searches in assembly graph the contig path (shown in red) that matches best with the site sequence \(x_3x_4x_5x_6\). Step 3. nanoGapFiller fills the gap with the nucleotide sequence of the best-matching contig path \(c_1c_3c_6c_{10}\)