The authors present AXIOME, an open-source software package for managing microbial ecology pipelines. AXIOME (formerly AutoQiime) was originally targeted for automating QIIME, an open source software package for comparison and analysis of microbial communities based on SSU ribosomal RNA. AXIOME currently includes support for mothur, a tool for comparison of microbial communities. Although these analyses can be automated via bash or python scripts, AXIOME provides a wrapper for both QIIME and mothur that takes an XML file as input and then automates the QIIME or mothur analysis of interest. AXIOME is implemented in C, Vala, R and Python and the architecture allows one to build customized research workflows centered around these existing software tools. In addition, AXIOME incorporates the BIOM universal data format, provides robust checkpointing and logging, and includes a companion GUI (Axiometic).

MAJOR COMPULSORY REVISIONS:

1. Efforts exist to integrate Qiime into Galaxy (https://github.com/qiime/qiime-galaxy), and a wrapper for mothur within Galaxy is currently available, yet were not referenced in the text. Additional discussion comparing & contrasting AXIOME to similar efforts that exist for automating QIIME & mothur within Galaxy is required.

2. The “Findings” section does not present any actual findings but instead details the functionality & rationale behind AXIOME. I recommend the authors move this text to a “Rationale” or “Functionality” section and then include a real example in the “Findings” section that involves a walkthrough of a combined QIIME/mothur analysis within AXIOME that highlights the ability build custom workflows that is currently lacking.

3. I failed to locate fine-grain details on the software architecture/design of AXIOME. This makes it very difficult to understand the relationship & individual roles of the Vala/C/R/python code contained in several files hosted on github. Additional detail required.

4. Line 67: “While effective, shell scripting can present a significant barrier to researchers using the software.” Additional detail required here to mention Galaxy and also discuss benefits offered by AXIOME over running these analyses within Galaxy.

5. Line 83: “Automation in AXIOME is essentially system-independent” Why essentially? Is it system-independent? If so remove ‘essentially’; otherwise, specify why not fully system-independent.

6. Line 89: “AXIOME currently fully manages QIIME [2] analyses and largely supports mothur [1].” What does AXIOME largely support? What doesn’t it support? Add more detail.

7. Line 90: “Integration with the phyloseq platform [4] will be part of future releases.” How would this tie-in with currently supported software? Clarify intent.

8. Line 94: Provide additional detail/clarify the following feature supported by AXIOME “…a technique for approximating high-dimensional data points as positive linear combinations of positive Components.”

MINOR ESSENTIAL REVISIONS

1. Other requirements in “Availability and Requirements” should list all required libs/packages/tools (Gee, NCBI blast2, etc)

2. Line 28: “…at least partially automated analysis.” Unclear what this means, clarify.

3. Line 56: “Axiometic, the companion GUI, simplifies XML script generation, further increasing usability of the software” Difficult to read, requires revision.

4. Line 64: “Typical analysis platforms… …which is available for essentially any software installed on a *nix-based operating system.” This sentence is difficult to read and I am unsure of the meaning, please revise.

DISCRETIONARY REVISIONS

• Recommend modifying Figure 1 to distinguish between novel features, those that are specific to mothur, and QIIME. Perhaps here is also where you could indicate future features.

• Recommend adding a second figure featuring the GUI.

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.

The revised manuscript is much improved. I appreciate all of the changes and additions the authors made to the manuscript. I only have two remaining minor revisions.

Minor Revisions

1. Line 67: Replace *nix with UNIX / Linux

2. Line 131: "AXIOME and the Galaxy project". Suggest changing section header to "Distinguishing features of AXIOME" or "Comparison to related work"

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.