Lynch et al. outline in their manuscript, "AXIOME: an open-source computational tool for automated exploration of microbial diversity", a tool that allows automated analysis using the very popular QIIME software package as well several other additional metagenomic methods. The manuscript and the software documentation are both concisely and clearly written. Also, my testing of the software did not reveal any obvious bugs during installation or during the use cases I tried.

Although AXIOME is not for everyone (LINUX users being its targeted audience), it does represent a significant add-on that would prove useful for users familiar with the methods already and need to automate tasks, as well as beginner users that can easily add parts of a pipeline together by using the AXIOMETIC GUI. The AXIOMETIC GUI seems a bit rough around the edges, but was straightforward to use after a few attempts. Improvement in the GUI and of course additional methods in the future would be ideal, and I believe using the open-source GitHub repository is a good step towards meeting these goals.

Discretionary Revisions

1. "open-source computational tool" is not really needed in the title. "AXIOME: automated exploration of microbial diversity" would probably suffice.

2. In the manuscript, I found the last paragraph on page 5 to be a bit too detailed and manual-like. For example the name of the template file (sample.vala), and 'aqxs' tool names are probably not needed and could be more generalized.

3. I think AXIOME and AXIOMETIC can probably be installable on a MAC, but the instructions seemed tailored towards a Linux (Ubuntu) OS. A small installation guide for Mac users would extend the number of potential users for AXIOME.

4. A more explicit comparison between the AXIOME (e.g. 'make') approach to automation compared to other existing automation methods such as the well-known 'Galaxy' software is needed. For example, the make approach allows separation between generating the pipeline and running the commands making (virtually every server has the make command installed already) resulting in a very portable and highly parallelizable system. Whereas something like Galaxy provides a nicer interface for novices, but requires a substantial amount of work to be installed thus forcing analyses to be more centralized onto a single server.

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.