The authors present an improved version of their Gigwa tool, highlight feature improvements and perform some performance tests and use cases. The authors demonstrate this is a substantial improvement on their prior version. The paper is clear and well-written, although could be more concise and focused on the major changes rather than listing all changes made. I have a few minor suggestions to improve the overall manuscript and tool: (1) I suggest removing the term "ergonomic" from the abstract and conclusion as this word does not capture well what the authors are attempting to communicate. (2) A webaddress to the tool in the abstract would be useful for readers to quickly access the tool rather than having to read down to the Conclusions to find the site. (3) I was expecting Gigwa to perform better than VCFtools, but this seems to only be the case for large datasets. Can the authors add more discussion on why VCFtools outperforms Gigwa? Are there other opportunities for Gigwa performance improvements? (4) The Gigwa site does not include any data on human populations. There are several reference human genome datasets that would be useful to add to the site (e.g., HapMap, 1000 Genomes).

Declaration of competing interests Please complete a declaration of competing interests, considering the following questions: 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? 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? Do you hold or are you currently applying for any patents relating to the content of the manuscript? 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? Do you have any other financial competing interests? 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.
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AUthors' response to reviews. Reviewer #1

We are grateful for sharing your experience with us.

A PDF documentation was available on the project homepage, but probably not so easy to find. We took the following steps to improve documentation visibility and help users understand how to use Gigwa:

• we converted the existing documentation to HTML, enriched it by adding further explanation and inserting screenshots where it seemed relevant, and embedded it within the web application so that it can be opened at any time from the main menu.

• we created 4 demonstration videos with embedded comments showing how to import data, filter data, manage outputs and efficiently use the phenotype-based discrimination feature.

• we mentioned the availability of those videos at the top of the HTML documentation where we also provided a link to the homepage.

• we also improved the Swagger documentation page by providing the full relative path to mentioned calls and adding a table providing terminology correspondence between the internal data model and those of the REST APIs.

Since the review, Gigwa V2 was presented at the International Plant and Animal Genome conference (PAG), and aroused interest of scientists from various countries and institutes. Since then we are having feedback from people installing it, so we are confident that the number of users is going to grow significantly.

Regarding the number of citations, we are aware of this concern and therefore we applied the following changes to V2:

• we added a reference to the original publication on the web application's homepage

• we made the system include a HOW_TO_CITE.txt file in each exported archive

We hope that all these improvements will help our tool gain visibility in the near future.

Reviewer #2

(1) Thank you for this suggestion. We removed the 3 occurrences of the word "ergonomic" and replaced them with "easy to use", "straightforward" and "user-friendly".

(2) We added the following sentence to the "Description" paragraph of the Abstract: "The project home page http://www.southgreen.fr/content/gigwa provides a list of live instances allowing to test the system on public data (or reasonably-sized user-provided data)."

(3) The Gigwa V1 manuscript explains this in the following terms: "VCFtools excels here because it is a C++ program working on flat files, which means that the time needed to access each record is negligible, whereas database engines need to obtain/deflate objects before manipulating them". An additional reason is that Gigwa being a 3-tier application, the application server (Java code) is at all time exchanging data with either the client-side UI (Javascript code) or the database server (MongoDB). Reducing this data exchange to a minimum is one of the main aspects on which we focused when optimizing our code. In other words, not being as fast as highly specific command-line tools is the downside of providing a web interface on top of structured data. In order to make this clearer to readers, we split apart Benchmark results and Benchmark discussion. In the latter, we referenced the explanation made in the previous article. We also mentioned in that paragraph a separate investigation focused on estimating the benefit of deploying MongoDB as a sharded cluster.

(4) The live Gigwa instance mostly put forward is the one hosted by CIRAD, on the southgreen.fr domain. Since South Green, our platform and network of bioinformaticians, focuses on tropical and Mediterranean crops, including human data there would not have made much sense. However, the instance hosted by the IRD institution (http://gigwa.ird.fr/) is more suitable for this kind of data as some teams there work on human health. So, we listed all live instances hosted by our network on the application's homepage, mentioned that in the abstract, and imported the Hapmap project's phase2+3's data into the IRD instance. This dataset was annotated using snpEff, linked to the UCSC genome browser, and enriched with individual's metadata to help users make the best of it.

The authors have adequately addressed my concerns. My only comment would be that I could not get the http://gigwa.ird.fr/ instance to load. It would be particularly interesting to look at human data on this site.

Declaration of competing interests Please complete a declaration of competing interests, considering the following questions: 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? 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? Do you hold or are you currently applying for any patents relating to the content of the manuscript? 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? Do you have any other financial competing interests? 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. We re-uploaded the manuscript file with only two modifications :

• an update of reference number 12 (recently accepted paper)
• the insertion of the RRID reference in the Availability and requirements section