The manuscript "Chromosomer: a reference-assisted genome assembly tool for producing draft chromosome sequences" by Tamazin et al. introduces a new reference-assisted assembly tool for large genomes., e.g. of a mammalian genome size.

The authors correctly indicate that with a large number of genomes being sequenced with NGS technologies it is possible to use assemblies of closely related species to estimate the order of scaffolds in de novo sequenced genomes. On the other hand, such an approach will likely produce errors in the regions where the de novo sequenced genome is different from the reference genome (lineage-specific structural differences).

The approach that authors chose is to use BLAST to place the target genome scaffolds on reference chromosomes. From the text, however, it is not clear what will happen when a target genome scaffold maps to more than one region of the reference genome. This likely to indicate two possible scenarios: a) the target genome scaffold is chimeric and the observed structural difference is not real or b) the target scaffold is correct and the structural difference is real. Because Chromosomer is not taking into account read mappings and does not in any way evaluates quality of target scaffolds and only uses one reference genome, it is unclear how exactly the tool deals with the structural differences between the reference and target genomes present inside the target genome scaffolds.

There are other mammalian genome-size reference assisted assembly tools., e.g. RACA (Kim et al., 2013) that take into the account read mappings and use more than one genome (reference and outgroup) to minimize the effect of chimeric scaffolds on reference assisted assembly, and to keep those structural differences that are well-supported either by read mappings or comparative data. The authors therefore, should compare the outcome of their tool to the outcomes of the reference assisted assembly tools built specifically for large genomes, like RACA.

On the other hand, Chromosomer transfers the annotation from reference genome to target predicted chromosomes. Again, there are tools that are built to do similar tasks (e.g., RATT). Therefore, the quality of annotation transfer needs to be evaluated and the results presented.

Level of interest

Please indicate how interesting you found the manuscript:
An article of importance in its field

Quality of written English

Please indicate the quality of language in the manuscript:
Acceptable

Declaration of competing interests
Please complete a declaration of competing interests, considering the following questions:
1. Have you in the past five years received reimbursements, fees, funding, or salary from an
organisation that may in any way gain or lose financially from the publication of this
manuscript, either now or in the future?
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose
financially from the publication of this manuscript, either now or in the future?
3. Do you hold or are you currently applying for any patents relating to the content of the
manuscript?
4. Have you received reimbursements, fees, funding, or salary from an organization that
holds or has applied for patents relating to the content of the manuscript?
5. Do you have any other financial competing interests?
6. Do you have any non-financial competing interests in relation to this paper?
If you can answer no to all of the above, write 'I declare that I have no competing interests'
below. If your reply is yes to any, please give details below.

I declare that I have no competing interests.

I agree to the open peer review policy of the journal. I understand that my name will be included
on my report to the authors and, if the manuscript is accepted for publication, my named report
including any attachments I upload will be posted on the website along with the authors'
responses. I agree for my report to be made available under an Open Access Creative Commons
CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments
which I do not wish to be included in my named report can be included as confidential comments
to the editors, which will not be published.

I agree to the open peer review policy of the journal.

Authors' response to reviews: (https://static-content.springer.com/openpeerreview/art%3A10.1186%2Fs13742-016-0141-6/13742_2016_141_AuthorComment_V1.pdf)

The authors have addressed the comments present in a previous review. However, the comparison with RACA has indicated that the presentation of the results and/or their interpretation needs to be modified. The text describing this comparison and the Figure 7 are misleading. It is unclear why the authors decided to apply the term "chromosomes" to the predicted chromosomal fragments (PCFs) RACA produces. PCFs in some cases could match complete chromosomes, but in many cases are only fragments of chromosomes (short or long) that RACA could assemble. Therefore the author's comparison of the tibetan antelope karyotype to RACA PCFs is not appropriate and is misleading (e.g., mentioning of an "ultra-short chromosome 10"). The fact that RACA detects two potential translocations involving cattle chromosomes is in my opinion a strong feature of RACA as it would only keep these rearrangements in PCFs if a strong support from raw read mappings exist for these positions and linking the adjacent syntenic fragments. On the other hand, to my understanding, Chromosomer is not expected to detect these events because the raw reads are not used in the analysis.

I would recommend that this issue is addressed in the next revision to avoid misleading the readers regarding the outcomes of the software the authors compare their tool to.

Level of interest

Please indicate how interesting you found the manuscript:
An article whose findings are important to those with closely related research interests

Quality of written English

Please indicate the quality of language in the manuscript:
Not suitable for publication unless extensively edited

Declaration of competing interests
Please complete a declaration of competing interests, considering the following questions:
1. Have you in the past five years received reimbursements, fees, funding, or salary from an
organisation that may in any way gain or lose financially from the publication of this
manuscript, either now or in the future?
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose
financially from the publication of this manuscript, either now or in the future?
3. Do you hold or are you currently applying for any patents relating to the content of the
manuscript?
4. Have you received reimbursements, fees, funding, or salary from an organization that
holds or has applied for patents relating to the content of the manuscript?
5. Do you have any other financial competing interests?
6. Do you have any non-financial competing interests in relation to this paper?
If you can answer no to all of the above, write 'I declare that I have no competing interests'
below. If your reply is yes to any, please give details below.

I declare that I have no competing interests.

I agree to the open peer review policy of the journal. I understand that my name will be included
on my report to the authors and, if the manuscript is accepted for publication, my named report
including any attachments I upload will be posted on the website along with the authors'
responses. I agree for my report to be made available under an Open Access Creative Commons
CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments
which I do not wish to be included in my named report can be included as confidential comments
to the editors, which will not be published.

I agree to the open peer review policy of the journal.

Authors' response to reviews: (https://static-content.springer.com/openpeerreview/art%3A10.1186%2Fs13742-016-0141-6/13742_2016_141_AuthorComment_V2.pdf)