Fig. 2 Combining Pore-C and assembly data for NA24385
We generated a draft assembly with Shasta using a flow cell of nanopore WGS data; the resulting contigs are plotted in length order. Next, using Pore-C virtual pairwise contacts and contigs as inputs, we generated scaffolds with 3D-DNA before a second round of scaffolding using SALSA2, followed by Purge Haplotigs to remove regional duplications. The resulting assembly shows high congruity with the reference genome (Fig. 2a). Fig. 2b shows scaffolding for chromosomes 3, 4 and 5. The top map shows contact density derived from Pore-C reads mapped against the draft assembly (length-ordered), and the bottom contact map is derived from the same Pore-C reads mapped against the final scaffolds. The combination of all three methods gives the best result, with a scaffold NG50 of 125 Mb. (Fig. 2c).