Overall, this is a very well written and organised review that provides an insiders perspective into the use of optical mapping for assembly validation and refinement.

Major Compulsory Revisions

1) It would be good to add more details about the use of optical mapping for improving MGSCv3. For example, how many discordant regions did not ultimately lead to a correction of the assembly? What were the explanations for these discordances and what was the breakdown for the various kinds of false-positive discordances? Does this suggest any areas where computational methods for Rmap assembly need improvement?

2) Where possible, please provide links to software that are mentioned in the text.

3) It is not clear to me how the following is possible: "In addition, the GRC curators are also applying optical mapping visualisation software to improve highly repetitive regions, where sequence alignments remain inconclusive and optical mapping data might be absent." How does MapSolver order in silico digests without any other information?

Minor Essential Revisions

1) "plants and vertebrate" -> "plants and vertebrates". Also, additional citations are needed here. 2) "The visual inspection of the" -> "Visual inspection of the". 3) This sentence is not very clear: "… generated by re-scaffolding Galgal4.0 with PacBio RS II sequence to optical mapping data using the same platform and mechanism". Is optical mapping data used after scaffolding with PacBio data? If so, rewording this sentence would help convey that better. 4) "… inter-chromosomal rearrangements in the reference assembly." Are the rearrangements likely to be misassembles? If so, it would be good to make that clear. 5) " … pinpointing of the location" -> " … pinpointing of their location" 6) "… these in to the …" -> "… these into the …"

Discretionary Revisions

1) " … genome assemblies due to the long range mapping information it provides." -> " ... genome assemblies aided by the long range mapping information it provides."

2) "… when being applied to vertebrate genomes" -> "… when applied to vertebrate genomes" 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 Research collaboration with Sciencewerke (distributor for OpGen) for the use of Optical Mapping data in genome assembly