Review for "Scaffolding and Completing Genome Assemblies in Real-time with Nanopore Sequencing"

Completed on 5 Oct 2016

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Comments to author

Author response is in blue.

This is a good paper and well laid out. I am particularly impressed by (a) the variety of datasets that the authors use, including generating their own and (b) the length of accurate scaffolding this approach takes.

However I have one major concern which must be addressed. The authors make much of their real time aspect of scaffolding. However real time algorithms and methods are only really valid if the entire workflow can be done in real time and stopped; as this method is a hybrid method with a batched based MiSeq run, it really is not at all practical as a real time method. In theory there is a marginal saving in ONT time, but as few people directly reuse a flow cell immedaitely, this is not really useful.

See response to Reviewer 1, point 1.

For me this should be recast as a prelude to future "all real time" methods rather than implying it could do something radical now. ie - I think it is fine to show the plots and the concept, but the authors should be up front by saying this is only really useful when the entire workflow can be stopped real time.

See response to Reviewer 1, point 1.

Minor comments

Line 23 "The major advancement..." - I would say "A..." or the "the key component of the technology...".

The phase is modified as “A key innovation of …”

I prefer "less data" to "fewer data"

We have revised as the reviewer suggested.

You need to provide the accession number of the MiSeq.

We have finalised the submission of the our datasets and the ENA accessions are now provided [page 10 column 1].