The manuscript by Yinan Wan, Istvan Albert, Moriah Szpara describes a viral genome assembly pipeline, based on Galaxy. The manuscript is well written and covers the overall complexity of genome assemblies. The provided solution, VirAmp, has a good documentation, the underlying software is open source. I really like the project but have a few suggestions to improve the usability.

Major Compulsory Revisions

As a Galaxy based platform I have expected that all tools are part of the Galaxy Tool Shed and that everyone will be able to install them easily to a local Galaxy instance from there. I can understand that the effort to create a proper Tool Shed integration is not negligible, but for such a project I would recommend to reconsider this option. The Tool Shed will enable an easy installation route to all kind of different platforms. This is for example essential to integrate the pipeline into an existing instance, thus increasing your user base. Furthermore, Tool Shed integration will enable real reproducibility on a tool level.

Galaxy also provides a very nice way to create workflows. I would like to see the described workflow as a real Galaxy workflow. Again, with a Tool Shed integration this could be extended to offer the workflow directly via the Tool Shed or on http://www.myexperiment.org/.

I know that Tool Shed Integration is disputable and I'm open to discuss this, but my major concern is that many of the described tools already exist in the Galaxy universe. Velvet and SPAdes are probably not perfect but they can be enhanced and I would rather see a collaboration to improve these tools, than a yet-again new version. BWA and BWA-mem are used by many instances, including usegalaxy.org and are actively supported and maintained and there are a lot of other tools that can be useful. Please consider to use and improve the already existing tools.

Minor Essential Revisions

For my minor concerns I created github issues, so we can discuss some points there.

• Assembler input fields shouldn't be optional https://github.com/ywan/viramp-project/issues/11
• Citations missing for a few tools https://github.com/ywan/viramp-project/issues/9
• An example workflow would be really cool! https://github.com/ywan/viramp-project/issues/8
• QC should be added to the Tool set https://github.com/ywan/viramp-project/issues/7
• docs.viramp.com should be in the top Help menu https://github.com/ywan/viramp-project/issues/6
• format argument is not needed in velvet https://github.com/ywan/viramp-project/issues/5
• "Paired-end reads" inputs are not clear defined https://github.com/ywan/viramp-project/issues/4
• Version informations should be added to each tool https://github.com/ywan/viramp-project/issues/3

Comments for the manuscript:

• Findings/Background: 4GB → 4 GB (also right before Conclusion)
• The step-headers are not styled the same way → “Coverage Reduction.” vs. “Deployment:”
• 1. Assembling: 'be used' vs 'is used'
• 1. There is a word, probably Galaxy, missing after the [3] reference.
• The line break is often right in the middle of HSV-1
• If INDEL is in Abbreviations, SNP should be also added

I would appreciate a short statement about any planned updates of tools and the overall service in the next years.

Kind regards, Bjoern

Level of interest An article whose findings are important to those with closely related research interests Quality of written English Acceptable Statistical review No, the manuscript does not need to be seen by a statistician. Declaration of competing interests I declare that I have no competing interests.

Authors' response: (http://www.gigasciencejournal.com/imedia/9832112691462111_comment.pdf)

Minor Essential Revisions: For a few days the server was not accessible and I got this error: "This job was killed when Galaxy was restarted. Please retry the job." This should be fixed and some mechanism should be implemented to prevent such large downtimes in the future.

Discretionary Revisions: I'm still thinking that QC is an essential part of every NGS pipeline and that FastQC or similar tools should be provided. Level of interest An article whose findings are important to those with closely related research interests Quality of written English Acceptable Statistical review No, the manuscript does not need to be seen by a statistician. Declaration of competing interests I declare that I have no competing interests.