The massive accumulation in sequencing project data calls for data management solutions that specifically focus on genomic variations. The authors present an infrastructure and associated front-end to serve those needs. The current focus appears to be an data retrieval, not so much on data interrogation. For example, while location information is provided (e.g. intergenic), it would be even more helpful to show all sequence variations in their genomic context as is frequently done in genomic viewers, where variations are added as tracks. The developed framework can be deployed at the user's site and is facilitated by the online demo version that nicely demonstrates the system's capabilities. Various export format options allow for flexible follow-up processing.

When testing Gigwa I found it a bit unintuitive in that I was not sure what operation triggers a new data retrieval and display. The detail information appearing when hitting the magnifying glass may benefit from a legend (what is PL, AC?). The zoom-able profile plots are very nice. Again, in conjunction with genome annotation - if available - would render the display more useful. Gigwa's performance feels "snappy" and robust (for the provided test data).

The manuscript is well written and describes the developed service with sufficient detail.

In summary, this reviewer believes that Gigwa can support genomics projects and will find its use.

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 (). 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: (http://www.gigasciencejournal.com/imedia/8415335892012167_comment.pdf)