1. The review article “Computational Methods for Genome Mapping” written by Lee Mendelowitz and Mihai Pop described the computational methods about how to align and assemble the single DNA molecular physical mapping data, it is a nice and well-written review article in respect of genome physical mapping using single molecular approach. As usually the dataset of the single molecular Rmaps or Nmaps is huge, and the complexity of computations in aligning and assembling this data is enormous, probably more complex than sequence assembling due to errors for single molecular measurements, and this review really capture the nature of the Rmaps or Nmaps, and described the various algorithms to deal with that. Therefore, it perfectly fits in the context of GigaScience, and I would highly recommend GigaScience to publish the review.

2. Another reason to publish this review article is that the single DNA molecular physical mapping (Optical mapping or nanocoding) become more and more important, because more and more genomes sequencing projects are using Next_gen sequencing platforms mainly Illumina sequencing, and the average sequence contig length is relatively small, mostly less than 100 Kb. Even with fragment pair-end sequencing reads available, the sequence contig length did get a little bigger, but hundreds or thousands of sequence gaps still exist. The assembled optical maps would definitely help to order and orient these sequence contigs, and characterize the sequence gaps. Thus, this review is a timely important review.

3. This review is a balanced review, and the authors made a thorough summary of each computational method in dealing single DNA molecule physical mapping, and point out what is the potential benefits and drawbacks, and this comment is fair and will help readers to test or choose computational methods for their own projects.

Minor Essential Revisions

There are several minor issues with the words or terms used in this review:

• Page 3, paragraph 2, “large DNA segment” is not wrong, but typically, “large DNA molecules” was used. Page 3, paragraph 2, “contain a number of errors such as in accurate estimates of fragment lengths or the deletion or concatenation of individual fragments” should be “ contain a number of errors such as inaccurate estimates of restriction fragment size, missing or extra restriction sites or missing small restriction fragments”

• Page 4, paragraph 1, “refer to the individual segment-sized maps as Rmaps” should be “refer to the single DNA molecule optical maps (the restriction fragments sized and ordered) as Rmaps.”

• Page 4, paragraph 1, “the assembled chromosome-length maps as consensus maps” should be “the consensus maps of the assembled Rmap contigs as optical consensus maps.”

• Page 9, paragraph 1, “random shearing” should be “randomly shearing”

• Page 9, paragraph 1, The sentence “The consensus map consists of one or more contigs, which are restriction patterns formed by stitching together overlapping optical maps” is not clear to me or readers

• Page 10, paragraph 2, in order to be consistent, “input maps” should be “input Rmaps” , “to cluster the maps based on similarity” should be “to cluster the Rmaps based on similarity” and so on… there are instances in this review should be corrected.

• Page 12, paragraph 1, “to produce a new set of consensus contigs” should be “ to produce a new set of Rmap contigs bearing updated optical consensus maps”

Level of interest An article of outstanding merit and interest 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