Fig. 1

The LongStitch pipeline. a Overview of the main steps of the LongStitch pipeline. The dashed border indicates the optional scaffolding step of ARKS-long. b Detailed schematic of the ntLink algorithm. (i) The input files to the ntLink long-read scaffolder are a draft assembly and long reads. (ii, iii) Minimizer sketches are computed for each of the input sequences (indicated by filled circles), then these minimizers are used to map the long reads to the draft assembly. Identical minimizers are vertically aligned, and also indicated by the vertical dotted line for one long-read. Each of the long-read mappings to the assembly can provide evidence about which contigs should be joined together, and in which orientation. (iv) After tallying all of the pairing information from the long reads, a directed scaffold graph is constructed, where the nodes are oriented contigs and the directed edges indicate long-read evidence between contigs. (v) Finally, the graph is traversed using abyss-scaffold to produce the final ordered and oriented scaffolds