Functional Metagenomic Analysis Tools

Question

[lotus28]

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.

Answer 1

[onestop_data]

Hi, I'm the creator of SUPER-FOCUS. Why do you think the tool lacks updates? I have been adding many new features asked by people all over the world.

What are your concerns? By the way, I will be using my blog to post about SUPER-FOCUS and other tools related to it.

[lotus28]

I am sorry, but I don't really remember what the actual issue was back then. I am glad to hear you keep supporting the tool

[onestop_data]

No problem. I'm more than happy to add new features that you may wish.