This is a very straight-ahead manuscript that follows in the work from Baylor and CSH to incorporate a diverse set of sequence/map resources for ensuring accurate and comprehensive sequence assembly. As such, many in the genomic community will benefit from the techniques and software developed by this group for achieving great improved assemblies, which may portend more useful reference genomes.

I might suggest that the authors consider more primary references to cite within their manuscript, especially concerning the Optical Mapping System, which my laboratory pioneered over last few decades.

Here's a few suggestions relevant to this quoted paragraph from the ms:
----"Another technology is optical mapping [12, 13], a method based on mapping the position of enzyme restriction sites along the sequence of the genome as observed by fluorescence microscopy, which recently has been automated to achieve high throughput solutions amenable to analysis of complex genomes. This technique allows the production of extremely long (hundreds of kbp) restriction maps which to date has been applied to: alignment to a reference sequence to identify structural variations [14–16], enhancing the genome assemblies of both prokaryotes [17, 18] and eukaryotes [19]."

****This paper from '98 reports the first automated Optical Mapping System:
Jing, J., Reed, J., Huang, J., Hu, X., Clarke, V., Edington, J., Housman, D., Anantharaman, T.S., Huff, E.J., Mishra, B., Porter, B., Shenker, A.,Wolfson, E., Hiort, C., Kantor, R., Aston, C., and Schwartz, D.C. Automated high resolution Optical Mapping using arrayed, fluid-fixed, DNA molecules. Proc. Natl. Acad. Sci. USA 95: 8046-8051, 1998.

This 2004 paper report an automated Optical Mapping, imaging station and microfluidic systems with application to human:
Dimalanta, E.T., Lim, A., Runnheim, R., Lamers, C., Churas, C., Forrest, D.K., dePablo, J.J., Graham, M.D., Coppersmith, S.N., and Schwartz, D.C. A microfluidic system for large DNA molecule arrays. Anal. Chem. 76: 5293-5301, 2004.

These papers, published some years ago, report applications of Optical Mapping to genome assembly, algorithm development and discernment of structural variants using a high-throuput Optical Mapping System:

Kidd, J.M., Cooper, G.M., Donahue, W.F., Hayden, H.S., Sampas, N., Graves, T., Hansen, N., Teague, B., Alkan, C., Antonacci, F., Haugen E., Zerr,T., Yamada, N.A., Tsang, P., Newman, T.L., Tüzün, E., Cheng, Z., Ebling, H.M., Tusneem, N., David, R., Gillett, W., Phelps, K.A., Weaver, M.,Saranga, D., Brand, A., Tao, W., Gustafson, E., McKernan, K., Chen, L., Malig, M., Smith, J.D., Korn, J.M., McCarroll, S.A., Altshuler, D.A.,Peiffer, D.A., Dorschner, M., Stamatoyannopoulos, J., Schwartz, D., Nickerson, D.A., Mullikin, J.C., Wilson, R.K., Bruhn, L., Olson, M.V., Kaul,R., Smith, D.R., and Eichler, E.E. Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56-64, 2008.

Church, D.M., Goodstadt, L., Hillier, L.W., Zody, M.C., Goldstein, S. She, X., Bult, C.J., Agarwala, R., Cherry, J.L., DiCuccio, M., Hlavina, W.,Kapustin, Y., Meric, P., Maglott, D., Birtle, Z., Marques, A.C., Graves, T., Zhou, S., Teague, B., Potamousis, K., Churas, C., Place, M.,Herschleb, J., Runnheim, R., Forrest, D., Amos-Landgraf, J., Schwartz, D.C., Cheng, Z., Lindblad-Toh, K., Eichler, E.E., Ponting, C.P., and The Mouse Genome Sequencing Consortium. Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biology 7(5):e1000112, 2009. Epub May 26, 2009. (Featured in Nature 459: 619, 2009, Research Highlights – “Genetics: Filling mouse holes”) Open access: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000112

Coleman, J.J., Rounsley, S.D., Rodriguez-Carres, M., Kuo, A., Wasmann, C.C., Grimwood, J., Schmutz, J., Taga, M., White, G.J., Zhou, S., Schwartz,D.C., Freitag, M., Ma, L., Danchin, E.G.J., Henrissat, B., Coutinho, P.M., Nelson, D.R., Straney, D., Napoli, C.A., Gribskov, M., Rep, M., Kroken,S., Molnár, I., Rensing, C., Kennell, J.C., Zamora, J., Farman, M.L., Selker, E.U.,Salamov, A., Shapiro, H., Pangilinan, J., Lindquist, E., Lamers,C., Grigoriev, I., Geiser, D.M., Covert, S.F., Temporini, E., and VanEtten, H.D. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genetics 5(8): e1000618, 2009; Epub Aug 28, 2009. Open access: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000618

Zhou, S., Wei, F., Nguyen, J., Bechner, M., Potamousis, K., Goldstein, S., Pape, L., Mehan, M., Churas, C., Pasternak, S., Forrest, D.K., Wise, R.,Ware, D., Wing, R., Waterman, M.S., Livny, M., and Schwartz, D.C. A single molecule scaffold for the maize genome. PLoS Genetics 5:e1000711, 2009. Open access: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000711

Teague, B., Waterman, M.S., Goldstein, S., Potamousis, K., Zhou, S., Reslewic, S., Sarkar, D., Valouev, A., Churas, C., Kidd, J., Kohn, S.,Runnhein, R., Lamers, C., Forrest, D., Newton, M.A., Eichler, E.E., Kent-First, M., Surti, U., Livny, M., and Schwartz, D.C. High-resolution human genome structure by single molecule analysis. Proc. Natl. Acad. Sci. USA, Jun 15; 107 (24):10848-53, 2010. Epub May 31, 2010. Open access: http://www.pnas.org/content/107/24/10848.full

Valouev, A., Zhang, Y., Schwartz, D.C., and Waterman, M.S. Refinement of Optical Map assemblies. Bioinformatics 22: 1217-1224, 2006.

Valouev, A., Li, L., Liu, Y., Schwartz, D.C., Yang, Y., Zhang, Y., and Waterman, M.S. Alignment of Optical Maps. J. Computational Biology13: 442-462, 2006.

Valouev, A., Schwartz, D., Zhou, S., and Waterman, M.S. An algorithm for assembly of ordered restriction maps from single DNA molecules. Proc. Natl. Acad. Sci. USA 103: 15770-15775, 2006.







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 Opgen, Inc. licenses patents from WARF that were filed by LMCG (my laboratory) covering Optical Mapping Technologies, algorithms and software.

Authors' response to reviews: (http://www.gigasciencejournal.com/imedia/1754464356188549_comment.pdf)

The reviewed version of the manuscript can be seen here:
http://www.gigasciencejournal.com/imedia/1719210328175779_manuscript.pdf
All revised versions are also available:
Draft - http://www.gigasciencejournal.com/imedia/1719210328175779_manuscript.pdf

The ms looks good and is ready for publication after a few discretionary revisions:
1-"Another technology is optical mapping [12–16], a method based on mapping the
position of enzyme restriction sites along the sequence of the genome as observed by
fluorescence microscopy, which recently has been automated [17, 18] to achieve
high-throughput solutions amenable to analysis of complex genomes"

Automation of Optical Mapping, as evidenced by these two citations, dating from 1998 and 2004 is not recent as described in this sentence. It is in fact--venerable. The authors may want to correct this mis-statement.

2- There is a recent PNAS paper (2015), from the Schwartz lab, that combines sequencing and Optical Mapping of several cancer genomes: http://www.pnas.org/content/112/25/7689.short , which could be included in the reference list here, both as an example of optical mapping complex genomes and ways to combine these analyses with sequencing.

3- The first paper reporting use of Optical Mapping for discovering structural variation was published in 2004, and might be worth citing here:
Zhou, S., Kile, A., Bechner, M., Place, M., Kvikstad, E., Deng, W., Wei, J., Severin, J., Runnheim, R., Churas, C., Forrest, D., Dimalanta, E.,Lamers, C., Burland, V., Blattner, F., and Schwartz, D. Single-molecule approach to bacterial genomic comparisons via Optical Mapping . J. Bacteriol. 186: 7773-7782, 2004. PMCID: PMC524920

4-Lastly, the method for preparing gel plugs/inserts for yeast was first published in 1984, and this might worth citing within the context of ms:
"Sample preparation
Yeast chromosomes for analysis in OpGen’s Argus system were prepared by a modification of the chromosome
embedment in agarose plugs procedure by Carle and Olson (Carle and Olson 1985)."

The 1984, Cell reference:
Schwartz, D.C. and Cantor, C.R. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37: 67-75,1984.





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 do not have any competing interests.

Authors' response to review: (http://www.gigasciencejournal.com/imedia/1760157902191230_comment.pdf)

The reviewed version of the manuscript can be seen here:
http://www.gigasciencejournal.com/imedia/1414544018188550_manuscript.pdf
All revised versions are also available:
First revision - http://www.gigasciencejournal.com/imedia/1414544018188550_manuscript.pdf

Minor Essential Revisions
Quick comment from their letter:

We agree with Reviewer 1. We have modified the text in order to remove the “recently” word.

Another technology is optical mapping [12–16], a method based on mapping the position of enzyme restriction sites along the sequence of the genome as observed by fluorescence microscopy, which can be automated...


—"can be" is incorrect—implies that it hasn’t been done, but may be possible ….. Suggest using : “…which was automated. The two citations buttress this view. I must insist on this change.


—Also the 2010 paper should remain in the reference list.

If the authors agree to make these minor changes, I’m okay with it being published.

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 Opgen, Inc. licenses patents from WARF that were filed by LMCG (my laboratory) covering Optical Mapping Technologies, algorithms and software.

The reviewed version of the manuscript can be seen here:
http://www.gigasciencejournal.com/imedia/1575354370191235_manuscript.pdf
All revised versions are also available:
First revision - http://www.gigasciencejournal.com/imedia/1575354370191235_manuscript.pdf