The manuscript describes a scaffolding tool and its use in scaffolding bacteria, yeast and a very large plant genome. I think the authors have done a fair job of exploring the parameter space of the presented tool, and I find the manuscript to be clearly written and mostly convincing. I like that the authors have coupled the publication of their fairly straight-forward, albeit useful, scaffolding tool with a new and interesting data type.

Thoughts/Comments:

(1) I would recommend putting Figure S1 in the main text, as it is critical to arguing that minion reads have error free k-mers long enough to be useful for scaffolding.

(2) I am somewhat skeptical that a k-mer based approach is the right one for scaffolding long, error prone reads. It seems to me that an alignment based approach would produce better results, as you can be more sure that the resulting linking of the scaffolds is the result of a true, contiguous, orthologous alignment. Have the authors explored this approach? I realize there are issues of efficiency to consider, however, I think for the volumes of minion reads currently available that this isn’t a big deal. Some nice tools, like marginAlign (see the Jain et al. paper), make higher quality alignments possible with nano-pore reads.

(3) It would be good to reference and discuss the Loman, Quick, Simpson paper on assembling E.Coli de novo from nano pore reads, which is available on Bio Arxiv. Clearly error correction can radically improve the utility of minion reads.

Level of interest An article of importance in its field Quality of written English Acceptable Statistical review Yes, but I do not feel adequately qualified to assess the statistics. Declaration of competing interests I declare that I have no competing interests.

Authors' response to reviewers: (http://www.gigasciencejournal.com/imedia/5046484471782784_comment.pdf)