Figure 3

Untangling complex regions. In the case of repetitive regions (represented by dark blue rectangles), the NaS workflow produced several contigs per MinION® template (Step3 and Step4). Indeed, the NaS read is fragmented, due to the indeterminate position of the repetitive region, contig2. Step5. Construction of the contig graph weighted with the seed-reads coverage of the given contig. Contig2, which represents the repetitive region, is linked to four different contigs. Step6. The contigs present in the path with the highest weight (contig1 – contig2 – contig3) are selected, using the Floyd-Warshall algorithm, and assembled to generate the final NaS read. Step7. The consistency of the synthetic NaS read is checked by aligning the initial Illumina reads set and detecting gap of coverage.