The manuscript "Computational Methods for Genome Ma pping" by Mendelowitz and Pop reviews several algorithms and tools for aligning and assembling optical mapping data. Two applications of genome mapping technology – SV detection and assisting genome sequence assembly – are then described, highlighting the importance of developing efficient tools for the analysis of these types of data.

Although the manuscript gives a comprehensive overview of the described methods, some information is missing and clarifications are needed.

Major Compulsory Revisions:

1. This review only deals with optical mapping as the creation of genomic restriction maps. However, some genome mapping techniques utilize methods such as nick translation reactions (mentioned briefly in the abstract). Since the manuscript's title refers to "Genome Mapping", it seems that these techniques should be addressed. Are the algorithms and tools mentioned applicable for other genome mapping techniques? Are there other tools available?

2. Alignment Methods: for each algorithm a detailed description of the scoring function is given. A general description of the basic concepts of these algorithms could be helpful, linking between the experimental procedure described in the introduction and the computational methods themselves.

3. Applications – Genome Assembly: what tools were used to construct the consensus optical maps compared to the genome assemblies from sequencing reads?

4. Applications – Genome Assembly: the introductory paragraph specifically addresses genomic repeats as a problem in genome assembly. It would therefore be appropriate to include a reference where optical mapping was used to solve such a problem, or to clarify where this was done in the referenced papers.

5. "There is, thus, a critical need for the continued development and public release of software tools for processing optical mapping data": throughout the manuscript the authors touch very lightly on the limitations of the different tools described. For most algorithms limitations and drawbacks are not mentioned at all, and a comparison between different algorithms is not given. It is thus unclear why the need for continued development is critical.

Minor Essential Revisions:

1. Figure 1 should perhaps be revised to include a typical image produced in an optical mapping experiment, to better clarify the scheme used to depict the common errors.

2. Figure 1d shows a sizing error due to an error in fluorescence intensity measurement, however fluorescent staining is not mentioned in the description given in the introduction. One of the two should be revised for clarity.