Aiming at non-bioinformaticians, Sempéré et al developed a web application 'Gigwa' for exploring and filtering large amounts of genotying data. Gigwa can handle multiple databases, can be deployed in either single or multi-user mode, and provides a variety of popular export formats.

I find that the Gigwa website is fast and easy and intuitive to use; it does exactly what the authors have described in the manuscript.

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major concerns
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However, users who wish to use Gigwa on their own data will have to install it locally. Installing and configuring Gigwa and required external softwares including MongoDB, JAVA and Tomcat is extremely difficult for non-bioinformaticians. Interested users can of course ask their system administrators to do the installation for them, but this will strongly limit the usage and popularity of Gigwa.

The authors did provide a website at which users can upload and analyse their own data; but login is required for data upload, and the registration is not open (interested users have to apply for an account by email).

I suggest that the authors should re-develop Gigwa into one of the following forms:

1. a web server that everyone can upload and explore their data, or
2. an all-in-one software bundle that includes all required softwares and comes with an intuitive, graphical and step-by-step installation guide (like LAMP; see ) ).

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

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Acceptable

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Authors' response to reviews: (http://www.gigasciencejournal.com/imedia/8415335892012167_comment.pdf) 

In response to my previous comments, the authors provided an all-in-one software bundle that includes Gigwa and all required softwares; this bundled version works under Windows and MacOSX.
In my opinion this would greatly promote the usage of Gigwa, especially in non-bioinformaticans. Thus all my concerns have been addressed.

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