This manuscript provides a useful, high level, reasonable review of the field of optical mapping as it relates to genome assembly and genome curation. Optical mapping is an important tool for characterizing and quality checking existing assemblies as well as for improving genome assembly. With so many whole genome shotgun projects underway, the topic is critically important and timely.

Because the article is a review, it is difficult to provide detailed criticism of the work. Therefore, I am only including some possible discretionary revisions because they seem to be important additions, but perhaps because of the space limitations for this article the level of detail already provided is all that is possible. All of the comments relate to places where it would be helpful to provide more detail.

Discretionary Revisions

1. Under the "Review" section, "To achieve this, optical consensus maps were aligned to the sequence assembly to identify 423 discordant regions, each of which was manually reviewed, resulting in 95 corrections."

It would be nice if the authors could a bit more detail about the nature of the corrections that were made. That would help the reader know more specifically the kinds of errors the optical mapping data are identifying.

1. Under the "Review" section, "This study also helped identify 322 errors in NCBI35...and demonstrated the concordance of optical mapping with the classical methods of genome assembly and analysis, i.e. fosmid end sequencing, paired-end mapping, microarray analyses and tiling array CGH."

Again, it would be helpful to know the kinds of errors that were identified by the optical mapping data. In addition, a more specific statement about how many "consistencies" were found with the assembly? Otherwise how can you say that it demonstrated concordance? I guess the authors are suggesting that because the original assembly was based on fosmid end sequencing, paired-end mapping, micro array analyses and tiling array CGH and that more errors weren't found that it demonstrates concordance? But the human sequence is also based on far more than just fosmid ends, etc. It is based on far more than just that. Perhaps the authors could make an even stronger statement about the strength of optical mapping here if they gave a sense of how much agreement there was? It's a little tough to fully understand which part of the study in reference [10] that they are referring to.

1. Under the "Review" section, the paragraph starting "More recently, optical mapping has been used..." Again most discussion about the specifics and difficulty of creating the Rmap itself would be helpful here.

2. Under the "Review" section, in the paragraph starting "The increasingly automated solutions used in the studies described above..." It seems helpful here to compare and contrast more between the different de novo assembly tools?

3. Under the "Review" section, sentence beginning "In an approach lying between the curation of ..." This is an awkward sentence that should be rewritten.

4. Under the "Review" section, paragraph beginning, "A recent return to assembled optical mapping..." A bit more detail on the Germinate & Grow section would be helpful, just a sentence or two.

5. Under the "Review" section, paragraph beginning, "In addition to the OpGen Argus platform..." A clearer explanation and comparison of the BioNano Genomics Irys' platform versus the others would be helpful.

6. Under the "Conclusions" section, paragraph starting with "Optical mapping provides genomic long-range information..." More detail on the success in generating de novo optical map assemblies and in generating assemblies integrating optical maps and sequence information would be useful.

7. Under the "Conclusions" section, "...but the variability of the detected size for identical fragments combined....remains an informatics challenge." Could a little more additional detail be provided on the specifics of what those informatics challenges are? Level of interest An article of importance in its field Quality of written English Acceptable 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.