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All of the recommended modifications were addressed and dealt with in a fashion to assist readability of the manuscript. The current form is acceptable to move forward in publication. I did have some initial reservations about the placement of the manuscript into PeerJ; however, the points made by the authors are acceptable and were addressed appropriately. The tools provided here will have utility in the community in resolving complex genome structures, and the example provided demonstrates how it may be used. Congratulations.
Considering some of the prior review comments and suggested edits provided for this manuscript, the current version is in pretty much acceptable condition for publication; however, after a read-through there were some suggested modifications as listed below.
The manuscript does provide valuable information which would help supplement genome assemblies and may provide a resource which may help generate new information to help move projects in a delayed-state due to assembly questions into a forward direction toward building complete genome resolution. I myself have been working with assembly data and would like to test the utility of the software scripts provided. The sample information provided here suggests some hope in addressing genome assembly issues. I applaud the efforts of the authors and feel that the software associated with this effort will have good utility within the research community.
One reservation that I may have is that this manuscript may be better destined for the Computational Science portion of PeerJ, rather than the biological side. The sample data was only marginally addressed on biological topics and the software attributes were more addressed here. I will approve this manuscript with the condition that the suggested edits are addressed as listed below:
Example of annotation:
LINE NO.: / PREVIOUS FORM / SUGGESTED FORM / [ADDITIONAL NOTES]
12: / It allows to / It allows one to / [ ]
14: / / / [ Line feed not needed within abstract. ]
18: / RGFA allows to design / RGFA allows one to design / [ ]
44: / allows to improve / allows one to improve / [ ]
56: / employing own custom fields / employing its own custom fields / [ ]
58: / of own analysis pipelines / of its own analysis pipelines / [ ]
61: / manually finishing assembly. / manually-done finishing assembly. / [ OR manually finished assembly. ?]
83: / segments: / segments; / [ a semi-colon should suffice here with no comma de-limited text following. /
88: / Segment and paths are stored in hash tables, which allow / Segments and paths are stored in hash tables, which allows / [ ]
92: / dead ends / dead-ends / [ ]
130: / which allow to retrieve the links / which allow one to retrieve the links / [ ]
145: / method requires to specify / method requires one to specify / [ ]
149: / E.g. / For example, / [Usually 'e.g.' would be used to shorten parenthesized text, this is used in a sentence. ]
167: / remain without link. / remain without a link. / [ ]
169: / it is one, / it is of the value 1, / [ ]
172: / allows to use any combination / allows one to use any combination / [ ]
173: / i.e. / / [ I would prefer to use “that is”, but the way it's used in both cases helps readability. ]
203: / except it is the only / except when it is the only / [ ]
213: / Then the coordinate / The coordinate / [ ]
214: / are those of v. / are also those of v. / [ ]
216. / are those of x. / are also those of x. / [ ]
226: / GFA graph from file / GFA graph from a file / [ ]
240: / 2.0 is installed. / 2.0, is installed. / [ OR Ruby system (version ≥ 2.0) ?]
246: / can e.g. be done / can for example be done / [ use in a sentence ]
246: / allows to modify / allows one to modify / [ ]
250: / GFA is a line based text / GFA is in a line based text / [ ]
253: / table / able / [ regarding the ability of 'diff' ]
278: / copy number, computed / copy number, and then computed / [ ]
291: / and B. (2015) / and B. (2015) / [ Is there a name that can be associated with B.? THIS CITATION SEEMS INCOMPLETE. ]
294: / (e.g. 28). / (e.g. reference 28). / [ ]
298: / cmin / / [should the cmin and lr* notation values be in a fixed font?]
337: / etc). / etc...). / [ ]
341: / allow to output their / allow the output of their / [ ]
368: / loosing part / losing part / [ ]
372: / sized datasets, / sized dataset, / [ ]
SPECIAL NOTE: There is heavy use of italicized text and fixed font usage within the manuscript which is important to convey meaning and ease legibility which should be preserved.
In many cases the use of 'one' was suggested, but may also be substituted with 'the user', 'a person', etc... ; 'one' is probably most simple, but conveys that an action will be done and assists readability.
A good manuscript. Congratulations!!
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