Review for "LINKS: Scaffolding genome assemblies with kilobase-long nanopore reads"

Completed on 8 Jun 2015 Sourced from : https://static-content.springer.com/open....

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Comments to author

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.