Inquiry regarding MetaPhlAn and HUMAnN versions used in the BAQLaVa preprint

Microbial community profiling BAQLaVa
1

hello, my name is Min-uk Park.

I recently read your bioRxiv preprint on BAQLaVa with great interest. I am currently planning to set up the BAQLaVa pipeline for my virome research, and I have a quick question regarding the tool setup.

1. Versions used in the preprint I understand that MetaPhlAn and HUMAnN are utilized within the pipeline (e.g., for bacterial depletion and profiling). Could you please specify exactly which versions of MetaPhlAn and HUMAnN (including their database versions) were used for the analyses in your preprint?

2. Recommended versions for setup As I am currently configuring my environment, are there specific versions of MetaPhlAn and HUMAnN that you strongly recommend to ensure the best compatibility and optimal performance with BAQLaVa?

Thank you for your time and for developing such an excellent tool. I look forward to your response.

Best regards,

Min-uk, Park

Seoul National University

2

The versions we recommend for BAQLaVa are HUMAnN 3.9, MetaPhlAn 4.1, and AnADAMA2 0.10.0, run with Python 3.10.

The manuscript workflow is slightly different than that above regarding MetaPhlAn for bacterial depletion, since MetaPhlAn v3.1.0 bacterial profiles already existed for these HMP2 samples - and we were thus able to use them to reduce computational requirements for bacterial depletion. However we recommend using the versions noted both above and in the readme!