I am going to perform functional analysis on a large collection of WGS gut metagenomes. However, options are too numerous. There is MEGAN6, MOCAT2, others. For me resource efficiency is key. I have discovered SUPER-FOCUS, that is claimed to be super-fast, but the lack of updates keeps me worried. Other things I am looking for are console-based interface, free license (unlike MEGAN) and platform agnosticism.
What are your tools of choice to derive functional features from WGS runs? Maybe, you have some specific experience using one of them and would like to share caveats, or you have actually compared outputs from several of them. I would be glad to hear out your advice.