The authors present an optical mapping analysis of two cell lines, one of which is diploid (GM12878 and one of the most studies cell lines of all time), and the other a cancer cell line. The optical mapping was performed using the Argus platform according to the manufacturer’s protocols, and then analyzed by the Argus optical mapper followed by alignment using the OPTIMA software. The authors then report on the quality of the optical maps as well as the mapping capabilities.
General Comments
1. The technical components and analysis process that the authors describe appears to be solid and I have no substantial critiques regarding the preparation of optical mapping DNA or the data processing.
2. I also find that the tables are useful for providing statistics on the maps and the process. However, there are no novel findings described in the work. I get the impression that the OPTIMA software tool is the most substantial component of the work, yet it appears to be submitted as a separate manuscript. It seems as though this manuscript should be included in the software manuscript to demonstrate its effectiveness and not stand alone.
Major Revisions
1. The analysis extends to alignment and then stops. In the summary and conclusions the authors state that the tool and the work in the manuscript can resolve large scale rearrangements and aid in de novo genome assembly; however the authors do not demonstrate any of that. If novel rearrangements can be discovered and they are shown in this work then I do believe it could stand as an independent manuscript. I would suggest the following specific additional analyses:
2. 1) identify known rearrangements / structural variation (or even insertion of sequence not present in the reference genome), basically anything that demonstrates the utility of the optical mapping. And then 2) to extend it to the cancer line which presumably has a number of additional rearrangements. Right not the analysis is incomplete and really needs these additional items to stand alone. The identification of these structural rearrangements should also have a figure describing them and connecting them with the optical image and mapping that is performed.
Discretionary Revisions
1. Lastly, 3) to re-enforce the claim of aiding in genome scaffolding I would suggest one or both of the following: a) chopping the reference genome into fragments in silico and showing they can be scaffolded back together, or b) (preferred) download a genome assembly in a non-scaffolded state (or take an ALLPATHS assembly for instance then breaking it by any stretch of N bases) and then scaffolding that. While the scaffolding portion is not absolutely necessary (and could probably be covered by further describing and referencing instances of optical mapping in scaffolding), it would be an analysis that would help a lot. However, the demonstration of structural rearrangement detection is a must for this manuscript to stand alone.

Level of interest An article of importance in its field
Quality of written English Needs some language corrections before being published
Statistical review No, the manuscript does not need to be seen by a statistician.
Declaration of competing interests I declare that I have no competing interests.

Authors' response to reviewers: (http://www.gigasciencejournal.com/imedia/1778312982193704_comment.pdf)

The reviewed version of the manuscript can be seen here:
http://www.gigasciencejournal.com/imedia/1569311312179937_manuscript.pdf
All revised versions are also available:
Draft - http://www.gigasciencejournal.com/imedia/1569311312179937_manuscript.pdf

As the authors pointed out the primary goal of a Data Note is to highlight and describe in detail a specific dataset and not to explore novel findings. The majority of my previous comments were on aspects that would fall outside of the scope of a Data Note (though I do think they would be interesting additional analyses). With the specifics of the Data Note format more clear to me, which are described by the journal as: "Data Notes highlight and help to contextualise exceptional datasets to encourage reuse. ... Data Notes focus on a particular dataset or sets, and provide detailed methodology on data production, validation, and potential reuse." many of my original critiques are no longer pertinent. The aspects that are relevant to the format were aspects that I believe were accomplished by the authors and clearly described in the manuscript.
Level of interest An article whose findings are important to those with closely related research interests
Quality of written English Acceptable
Statistical review Yes, but I do not feel adequately qualified to assess the statistics.
Declaration of competing interests I have no competing interests.

The reviewed version of the manuscript can be seen here:
http://www.gigasciencejournal.com/imedia/7524659831937050_manuscript.pdf
All revised versions are also available:
First revision - http://www.gigasciencejournal.com/imedia/7524659831937050_manuscript.pdf