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Fig. 6 | BMC Bioinformatics

Fig. 6

From: SLR: a scaffolding algorithm based on long reads and contig classification

Fig. 6

(a) There are six long reads: lr1, lr2, lr3, lr4, lr5, and lr6. The contigs c1 and c2 are aligned with lr1. c3, c4 and c5 are aligned with lr2. c6, c4 and c7 are aligned with lr3. c7, c8 and c9 are aligned with lr4. c10, c11 and c12 are aligned with lr5. c9, c11, c13 and c2 are aligned with lr6. We assume that all these alignments are forward, and all contigs are longer than Lca. (b) Based on the alignment result described in (a), SLR obtains six local scaffolds: ls1, ls2, ls3, ls4, ls5, and ls6. (c) The scaffold graph G1 is built using all contigs. We find that G1 is complicated. (d) Based on the contig classification method described in Section 2.2, the contigs can be divided into two categories. Because c4 is located in the middle position of ls2 and ls3 and has two distinct 3’-end neighbours and two distinct 5’-end neighbour contigs, it is identified as an ambiguous contig. c11 is also an ambiguous contig. The remaining contigs are identified as unique contigs. The scaffold graph G2 is built based on unique contigs and is thus less complicated than G1

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